Process Description
P-Value Quantile Plotter
| Welcome to JMP Genomics |
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| Getting Started with JMP Genomics |
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| System Requirements |
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| Text Conventions |
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| The Genomics Main Menus |
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| The File Menu |
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| The Genomics Starter |
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| Important Differences between JMP and JMP Genomics Dialogs |
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| Running a Process |
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| Tabbed Reports |
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| Stopping a Process |
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| Saving and Loading Settings |
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| SAS Variable Names and Labels |
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| Files and Data Sets |
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| SAS Data Sets |
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| Experimental Design File (EDF) |
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| Data Sets Used in JMP Genomics Processes |
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| Sample Case Studies |
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| The JMP Genomics Starter |
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| Current Study |
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| Studies |
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| Import |
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| Experimental Design File |
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| Affymetrix |
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| Illumina |
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| Nanostring |
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| Other Expression |
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| Other Genetics |
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| Proteomics |
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| Next-Gen Sequencing |
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| Text |
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| Summarize |
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| Workflows |
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| Basic |
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| Advanced |
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| Genetics |
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| Genetics Utilities |
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| Relatedness Measures |
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| Genetic Marker Statistics |
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| GWAS Testing |
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| Other Association Testing |
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| Haplotype Analysis |
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| Model-free Linkage |
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| Linkage Maps and QTL |
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| Breeding Analysis |
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| Copy Number |
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| Spectral Preprocessing |
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| Expression |
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| Quality Control |
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| Normalization |
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| Normalization (Next-Gen) |
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| Differential Expression |
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| Expression Utilities |
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| Pattern Discovery |
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| Predictive Modeling |
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| Main Methods |
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| Model Comparisons |
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| Predictive Modeling Utilities |
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| Subgroup Analysis |
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| P-Value Operations |
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| Genome Views |
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| Genome Browser |
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| Track Creation |
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| Annotation Analysis |
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| General |
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| Affymetrix |
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| Ingenuity |
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| GSEA / MSigDB |
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| SAS Data Set Utilities |
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| Tables |
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| Rows |
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| Columns |
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| Import/Export |
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| General Utilities |
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| Documentation and Help |
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| The Menu Bar |
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| Add Study |
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| Manage Genomics Studies |
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| View Study Metadata |
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| Assign Default Data Sets |
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| Assign Wide Variable Roles |
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| Imputed SNP Import Tutorial |
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| Basic Genetics Workflow |
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| Basic Linkage Mapping Workflow |
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| Basic Copy Number Workflow |
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| Basic Exon/Alternative Splicing Workflow |
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| Basic Expression Workflow |
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| Basic miRNA/miRNA-Seq Workflow |
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| Basic RNA-Seq Workflow |
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| Basic Tiling Workflow |
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| Genetics Rare Variants Workflow |
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| Genetics Q-K Analysis Workflow |
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| Expression QC Workflow |
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| Expression Statistics Workflow |
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| Workflow Builder |
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| Journal Builder |
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| Variable Gene Selection |
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| Evaluation of Normalization Methods |
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| Introduction to Predictive Modeling |
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| Customize Genomics Starter |
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| Register Add-ins |
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| R Package Manager |
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| Generate Genomics Dialogs |
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| JMP Genomics Programming Guide |
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| Getting Started |
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| The Column Contents Process |
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| The Anatomy of a JMP Genomics Analytical Process |
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| Adding and Deleting JMP Genomics Analytical Processes |
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| JMP Genomics XML Tags, Attributes, and Values |
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| The Column Contents Process |
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| JMP Genomics XML tags, Attributes, and Values |
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| Symbols |
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| Writing your XML Code |
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| Example: A Process for Creating a SAS Data Set |
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| The Import Individual Text, CSV or Excel Files Process |
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| SAS Code for the Import Individual Text, CSV, or Excel Files Process |
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| XML Code for the Import Individual Text, CSV, or Excel Files Process |
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| Creating a JSL File for Dynamic Graphics and Analyses |
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| The Distribution Analysis Process |
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| SAS Code for Generating JSL |
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| Macros Available for JMP Genomics Processes |
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| Macro Descriptions |
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| Writing High Quality Processes |
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| Audience |
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| Development Tips |
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| Code Reuse |
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| Improving Your SAS Macro Language Skills |
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| Line and Macro Length Limits |
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| Additional Resources |
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| Introduction |
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| AceView Database |
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| Annotation Summary |
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| Change Significance Criterion |
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| Check Variable Requirement and Usage |
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| Close All |
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| Cluster Domains |
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| Construct One-way Plots |
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| Contingency |
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| Contingency Analysis |
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| Create Subset Experimental Design Data Set |
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| Create Subset Experimental Design Data Set, Excluding Selected Curves |
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| Create Subset Genotype and Annotation Data Sets |
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| Create Subset with Mean Difference and P-value Criteria |
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| dbSNP |
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| Describe Output |
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| Dot Plot |
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| Enter new -log10(p) cutoff |
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| Entrez Cross |
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| Entrez Gene |
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| Exclude Markers and Rerun Analysis |
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| Fit Incidence Density Model |
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| Fit Model and Plot LS Means |
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| Fit Survival Model to Input Data for Selected Rows |
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| Forest Plot |
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| Forest Plots of Credible Intervals |
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| GenBank Nucleotide |
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| Gene List |
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| Generate Report |
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| Genotype |
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| GO Stat |
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| Graph Time Trends |
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| Graph Trellis Plot |
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| IPA Upload |
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| iPathwayGuide Output Data |
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| Launch Interactive LD Plots for R^2 |
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| Launch JMP Genomics Browser |
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| Launch Plot Intensities |
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| Linkage Group X |
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| Malecot LD Map |
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| Odds Ratio Plot |
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| Onto-Express |
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| Open Subset in Tall Format |
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| Open Subset in Wide Format |
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| Partial Correlation Diagram |
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| Plot Fixed Effect Components |
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| Plot Oneway Means by Chromosome Position and Overlay Tracks |
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| Plot Survival Curves for Stratified Data |
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| Plot Trait by Genotype |
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| PubMed |
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| Reopen Dialog |
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| Reverse Linkage Group Marker Orders |
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| Revert Clustering |
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| Save Current Linkage Group Membership |
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| Select Markers in Graphs or Linked Tables, then Click to View Survival Curves |
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| Show Duplicates |
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| Show Rows in Heat Map |
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| Subset and Transpose |
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| Autocorrelation Plot |
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| Bar Chart |
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| Box Plot |
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| Bubble Plot |
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| Cell Plot |
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| Chart |
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| Contingency Plot |
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| Contingency Table |
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| Contour Plot |
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| Correlogram |
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| Dendrogram |
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| Distance Graph |
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| Distribution |
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| Forest Plot |
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| Geographical Map |
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| Hazard Ratio Event Plot |
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| Heat Map and Dendrogram |
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| Histogram |
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| LD Decay Plot |
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| MA Plot |
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| Manhattan Plot |
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| Matched Pairs Analysis |
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| Mosaic Plot |
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| One-way Plot |
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| Overlay Plot |
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| Parallel Plot |
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| Principal Components Analysis Plot |
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| Q-Q Plot |
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| Receiver Operating Characteristics (ROC) Curves |
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| Reliability Diagram |
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| Scatterplot |
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| Scree Plot |
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| Segmentation Summary Plot |
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| Shift Plot |
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| Standardized Residual Plots |
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| Surface Plot |
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| Survival Curves |
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| Survival Plot |
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| Time Series Graph |
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| Trace Plot |
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| Tree Map |
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| Trellis Plot |
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| Volcano Plot |
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| Waterfall Plot |
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| Annotation Data Sets |
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| Combine this Study with Study from Update Tab |
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| Combine with: |
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| Combined Study Name |
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| Default Annotation Data Set |
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| Default Wide Input Data Set |
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| Default Experimental Design Data Set |
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| Default Tall Input Data Set |
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| Delete study |
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| Dependent Variable |
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| Experimental Design Data Sets |
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| Folder of Annotation Study Data Sets |
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| Folder of Experimental Design Study Data Sets |
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| Folder of Tall Study Data Sets |
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| Folder of Wide Study Data Sets |
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| Input SAS Data Set |
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| Label Variable |
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| List-Style Specification of Lock-In Categorical Predictor Variables |
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| List-Style Specification of Lock-In Class Predictor Variables |
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| List-Style Specification of Lock-In Continuous Predictor Variables |
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| List-Style Specification of Predictor Categorical Variables |
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| List-Style Specification of Predictor Continuous Variables |
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| Lock-In Categorical Predictor Variables |
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| Lock-In Class Predictor Variables |
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| Lock-In Continuous Predictor Variables |
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| New Study Name |
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| Output Folder |
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| Predictor Categorical Variables |
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| Predictor Continuous Variables |
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| Server Output Directory |
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| Study |
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| Study Name |
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| Tall Data Sets |
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| Wide Data Sets |
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| Weight Variable |
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| UNNAMED (Blank is a delimiter) |
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| UNNAMED (Parse from left) |
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| Additional New Design Variable Names |
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| Affection Status Coding |
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| Allele Delimiter |
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| Allele Peaks Data Set |
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| Alleles to Use for Genotypes |
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| Allocate Memory Size |
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| Alternate Phenotype File |
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| Annotated Variants within Known Genes (gene) |
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| Annotation Columns |
|
| Annotation Data Set |
|
| Annotation File |
|
| Annotation Gene Name Variable |
|
| Annotation Merge Variables |
|
| Annotation SAS Data Set |
|
| Apply log2 transformation to intensities |
|
| Apply original column names |
|
| ArrayTrack Annotation Output Data Set |
|
| ASM Files from Version of Assembly Pipeline prior to 2.0 |
|
| Background Correction |
|
| Background Correction Method |
|
| Background Subtraction |
|
| Barcode File to Import |
|
| Baseline Reference Data Set |
|
| Baseline Reference SAS Data Set |
|
| Baseline Variable |
|
| BIM File |
|
| Bin Method |
|
| Bin Size |
|
| Bin Summary Statistic |
|
| Binary PED File |
|
| Binding Density QC |
|
| By Variables |
|
| Cast Selected Columns into Roles |
|
| Cel Layout File |
|
| CGA Tools testvariants File |
|
| Channel Status |
|
| Check available disk space |
|
| Check uniqueness of column names |
|
| Choose a folder containing files listed in the File column |
|
| Chromosome |
|
| Chromosome Summary Data Set |
|
| Chromosome Variable |
|
| CN Columns to Include |
|
| CN Measurements to Include (100K or 500K Arrays) |
|
| Code genotypes numerically |
|
| Column Delimiter |
|
| Column Delimiter for Genotype Probability File(s) |
|
| Columns to Include |
|
| Columns to Include In Output Data Set |
|
| Combine multiple VCF files into a single data set |
|
| Compress output data sets |
|
| Compute Reference Scaling Factor |
|
| Continuous Variables to Summarize |
|
| Control Gene Normalization |
|
| Copy Number Annotation Data Set |
|
| Copy Number Annotation SAS Data Set |
|
| Copy Number Data Set |
|
| Copy Number File |
|
| Count Data |
|
| Count of Variations by Gene (geneVarSummary) |
|
| Count reads by strand |
|
| Covariate File |
|
| Covariate File has a Header Row |
|
| Create Combined Data Set |
|
| Create Quality Flag Data Set |
|
| Create separate data sets for B_Allele_Freq and/or Log_R_Ratio |
|
| Create separate data set(s) for each chromosome when there are more variants than: |
|
| Create separate data sets for each selected measurement |
|
| Create separate data sets for SNP- and CN-summarized probesets |
|
| Create wide Output Genotype Data Sets |
|
| Cross Type |
|
| Custom File Filter Expression |
|
| Customer Array |
|
| Cut-off for DP |
|
| Cut-off for GQ |
|
| Data File |
|
| To Specify a Data File Type: |
|
| Data Set Containing Probes to Remove |
|
| Data Start Row |
|
| Data Step Statements |
|
| Delimiters |
|
| Detection p-Value Cutoff for Setting Individual Intensities to Missing |
|
| Display marker genotype cell color plots |
|
| Drop SNPs with this percentage of samples that are below: |
|
| Encoding of Raw Array Files |
|
| End |
|
| Exclude rows with missing physical position |
|
| Exon Count |
|
| Exon Ends |
|
| Exon Starts |
|
| Experimental Design Data Set Corresponding to Baseline Reference Data Set |
|
| Experimental Design File |
|
| Experimental Design SAS Data Set Corresponding to Baseline Reference SAS Data Set |
|
| Exponential Multiplier of Kernel Density |
|
| Expression |
|
| FAM File |
|
| Feature Identifier |
|
| Feature Identifier for Computing Counts |
|
| File Filter Expression |
|
| File Type |
|
| Files for Variants Call |
|
| Files in PBAT Format |
|
| Filter before: |
|
| Filter out genes with detection p-value above: |
|
| Filter to Exclude Chromosomes |
|
| Filter to Include Chromosomes |
|
| Filter to Include Annotation Rows |
|
| Filter to Include Gene Model Rows |
|
| Filter to Include Markers |
|
| Filter to Include Observations |
|
| Flag Filter Expression |
|
| Folder Containing a FASTA-formatted Reference Sequence |
|
| Folder Containing Other Library Files |
|
| Folder Containing Raw Data Files |
|
| Folder Containing Raw Sequence Files |
|
| Folder Containing Rterm.exe |
|
| Folder Containing the BPMAP Files |
|
| Folder Containing the CDF File |
|
| Folder Containing the Library Files |
|
| Folder Containing the Meta Probeset File |
|
| Folder Containing the RCC Data Files |
|
| Folder of BAM Files |
|
| Package or Individual Genome Folder Containing ASM Results |
|
| Folder of Data Files from Eland |
|
| Folder of Feature-Barcode Matrices |
|
| Folder of Illumina Data File |
|
| Folder of Input Files |
|
| Folder of Raw Array Files |
|
| Folder of Raw BAM Data Files |
|
| Folder of Raw Data Files |
|
| Folder of Raw Files |
|
| Folder of Raw SAM Data Files |
|
| Folder of Samples File |
|
| Folder of SNP/DIP Detection Table CSV Files |
|
| Folder of Track Gene Text Settings Files |
|
| Folder of VCF Files |
|
| ...for at least this percentage of the samples |
|
| GC Score Cutoff |
|
| Gene File to Import |
|
| Gene Identifier |
|
| Gene Model Text File |
|
| Genotype Data Set |
|
| Genotyping Error Threshold |
|
| Genotype File |
|
| Genotype Files |
|
| Genotype Probability File(s) |
|
| Genotype Probability Threshold |
|
| Genotyping Calls Data Set |
|
| Get all column names from first row |
|
| Get Breadth of Coverage |
|
| Housekeeping Genes |
|
| How shall I get the information about your experiment |
|
| ID Variables |
|
| ID Variables to Keep |
|
| Illumina Data File |
|
| Imaging QC |
|
| Import CEL intensities without merging annotation |
|
| Include intron bins |
|
| Include MM in output |
|
| Include sequence data in output |
|
| Include SNP variants only |
|
| Increase R Software Memory Limit |
|
| Indicator of Different Column Names across Raw Data Files |
|
| Individual Variables |
|
| Input Arlequin File |
|
| Input Data Set |
|
| Input NEXUS File |
|
| Input OneMap File |
|
| Input Pedigree File |
|
| Input Phenotype File |
|
| Input SAS Data Set |
|
| Input SAS Data Set |
|
| Input WinQTLCart File |
|
| Intensity Variables to Bin |
|
| Keep single probes not associated to any probeset |
|
| Keep single-probe-sets not associated to any transcript cluster |
|
| Key Variable(s) to Merge with Input Data Set |
|
| Key Variable(s) to Merge with Input SAS Data Set |
|
| Length of Sample ID Column |
|
| LGEN File |
|
| List of Phenotype Variable Names |
|
| List of Variable Names |
|
| List of Variable Names and Lengths |
|
| List of Variable Names and Types |
|
| List-Style Specification of Housekeeping Genes |
|
| List-Style Specification of Individual Variables |
|
| List-Style Specification of Intensity Variables to Bin |
|
| List-Style Specification of Marker Variables |
|
| List-Style Specification of Trait Variables |
|
| List-Style Specification of Variables to be Included for Normalization |
|
| LOH Columns to Include |
|
| LOH Measurements to Include (100K or 500K Arrays) |
|
| Map Data Set |
|
| Map File |
|
| MAP Files |
|
| Marker Data Set |
|
| Marker ID Variable |
|
| Marker Label |
|
| Marker Name Variable |
|
| Marker Type |
|
| Marker Variables |
|
| Master Variations (masterVarBeta) |
|
| Matrix File to Import |
|
| Maximum Column Length |
|
| Maximum Intron Bin Size |
|
| Measures to Include (Chromosomes Data) |
|
| Measures to Include (CopyNumber Data) |
|
| Measures to Include (SNP6 Array) |
|
| Merge Variables |
|
| Meta Probeset File |
|
| MiniML-formatted File |
|
| Minimum Number of Columns to Scan |
|
| Minimum Number of Probes to Summarize Probe-Set Level |
|
| Missing Covariate Value |
|
| Missing Genotype Value |
|
| Missing Individuals Threshold |
|
| Missing Phenotype Value |
|
| Missing Quantitative Trait Value |
|
| Name of Phenotype Variable |
|
| Names of Variables Preceding Genotype Probability Columns |
|
| NBeads Output Data Set |
|
| Negative Control Method |
|
| New Study |
|
| New Variable Names for Experimental Design |
|
| No Family ID Column |
|
| No Parent ID Columns |
|
| No Phenotype Column |
|
| No Sex Column |
|
| Normalization |
|
| Normalize copy number data using autosomes |
|
| Normalize SNP data using autosomes |
|
| Number of CEL Files to Process at a Time |
|
| Number of Channels in Each File |
|
| Number of Data Files to Process at a Time |
|
| Number of Genotype Probability Columns |
|
| Number of Genotype Probability Columns per Individual |
|
| Number of Rows in Each Bin |
|
| Number of Rows to Scan |
|
| Options |
|
| Order Annotation Data Set by SNP column order |
|
| Output Allele Intensity Data Set |
|
| Output Allele Intensity Experimental Design Data Set |
|
| Output Annotation Data Set |
|
| Output Copy Number Intensity Data Set |
|
| Output Data Set |
|
| Output Data Set Name |
|
| Output Data Set of Normalization Factors |
|
| Output Data Set of Selected Stable Genes |
|
| Output Expected Genotype Data Set |
|
| Output Experimental Design Data Set |
|
| Output File Name |
|
| Output File Prefix |
|
| Output Folder |
|
| Output Genotype by Chromosomes |
|
| Output Genotype Data Set |
|
| Output Genotype Probabilities Data Set |
|
| Output Genotype Threshold Data Set |
|
| Output Map Data Set |
|
| Output Probe-level Intensity Data Set |
|
| Output Sequence Data Set |
|
| Output SNP-summarized Copy Number Intensity Data Set |
|
| Output Wide Data Set |
|
| p-Value Cutoff for Segregation Test |
|
| Parent 1 ID Variable |
|
| Parent 2 ID Variable |
|
| Parse Associated Gene Column |
|
| PDF or RTF Output File |
|
| PDF Output File |
|
| PDF Output File Name |
|
| PED or FAM Files |
|
| Pedigree File |
|
| Percentage of Data to Be Included in Training Data |
|
| Percentage of Samples Below Cut-off(s) for Dropping SNPs |
|
| Percentage of samples for dropping SNPs |
|
| Perform log2 transform |
|
| Perform log2 transform after scaling |
|
| Phenotype File has a Header Row |
|
| Ploidy Level |
|
| Ploidy Type |
|
| PM Correction |
|
| Position |
|
| Position Variable |
|
| Positive Control Limit of Detection QC |
|
| Positive Control Linearity QC |
|
| Positive Control Method |
|
| Prefix for New Columns |
|
| Prefix for Output Data Set Names |
|
| Prefix for Output Experimental Design Data Set Names |
|
| Prefix for SNP Names |
|
| Prefix to Append to SNP Column Names |
|
| Prefix to Append to SNP Column Names (for Full Data Table) |
|
| Prefixes of SNPs to Include in Data Sets |
|
| Probe Coordinates Output Data Set |
|
| Probe Group File |
|
| Probe Normalization |
|
| Probe Normalization Method |
|
| Probeset File |
|
| Probeset Variable |
|
| Probe Variable |
|
| QC Control File |
|
| QC Output Data Set |
|
| QC Probe Output Data Set |
|
| Quality Flag Output Data Set |
|
| Quantitative Variables |
|
| Reference File |
|
| Reference Gene Normalization |
|
| Reference Genes to Use |
|
| Reference Genome File |
|
| Remove AFFX Control SNPs from output data set(s) |
|
| Remove Control Genes |
|
| Remove PCR duplicates |
|
| Remove Reference Genes in Output |
|
| Row Number of Variable Names |
|
| Sample File |
|
| Sample File |
|
| Sample Files |
|
| Sample Variable |
|
| SAS Code for Customized Flagging Rule |
|
| SAS Code to Create Columns |
|
| SAS Code to Create New Design Variables |
|
| Save as SAS Data Set |
|
| Scaling Factor |
|
| SD Output Data Set |
|
| Segments CN Data Set |
|
| Segments CNNeutralLOH Data Set |
|
| Segments LOH Data Set |
|
| Segments Mosaicism Data Set |
|
| Segments NormalDiploid Data Set |
|
| Select an array |
|
| Select Column to Parse |
|
| Select Files |
|
| Select key variable to merge files |
|
| Select the folder containing .ARR files |
|
| Select the folder containing pairs of ARR and data files |
|
| Select the type of file(s) to input |
|
| Selected Column |
|
| Server Output Directory |
|
| Set flagged data to missing |
|
| Set heterozygous to missing |
|
| Set individual genotypes to missing that are below: |
|
| Shifting Factor |
|
| Smoothing Bandwidth Multiplier |
|
| SNP Annotation Data Set |
|
| SNP Annotation SAS Data Set |
|
| SNP Map File |
|
| Sort genotype columns and map rows |
|
| Source of Files |
|
| Specify the maximum number of missing genotypes for a locus to be included in the output data set |
|
| Specify your Input File |
|
| Spot Coordinates Output Data Set |
|
| Start |
|
| Strand |
|
| Study |
|
| Summarization Method |
|
| Summary Level |
|
| Summary Method |
|
| Tab-Formatted Probe Sequence File |
|
| Track Gene Text Setting File |
|
| Trait Variables |
|
| Transformation Method |
|
| Type of Array |
|
| Type of File |
|
| Type of File(s) |
|
| Type of File Conversion |
|
| Type of Map Files |
|
| Type of Other Files |
|
| Type of PED/FAM and Other Files |
|
| Type of Phenotype Variable |
|
| Unit for Genetic Distance |
|
| Value of Chromosome Variable Indicating Non-autosomes |
|
| Value of Columns Above to Be Associated with Non-autosomes |
|
| Variables By Which to Merge Annotation Data |
|
| Variables Containing Primary Data |
|
| Variables to be Included for Normalization |
|
| Variables to Keep in Output Data Set |
|
| Variations (var) |
|
| Variations at Known db SNP Loci (dbSNPAnnotated) |
|
| Weighted with Kernel Density |
|
| What kind of data files do you have? |
|
| What type of Experiment is this? |
|
| Width of Positional Bin |
|
| Accession Number Variable |
|
| Add Fold Change Filter to Select Significant Tests |
|
| Add Marker Genes to Explore |
|
| Add Mean Difference Filter to select significant tests |
|
| Additional Bandwidth on Each Side of Tracks |
|
| Additional Fixed Effects |
|
| Additional Random Effects |
|
| Adjustment Effects |
|
| Allele Characters for A (P1 line) and B (P2 line) |
|
| Alpha |
|
| Alpha value for Beta distribution |
|
| Analyze rare variants only |
|
| Annotation Analysis Group Variable to Use |
|
| Annotation Analysis Group Variable |
|
| Annotation Analysis Group Variable for Collapsing Rare Variants |
|
| Annotation Analysis Group (Gene e.g.) Variable |
|
| Annotation Chromosome Variable |
|
| Annotation Group Variable |
|
| Annotation Input SAS Data Set |
|
| Annotation Label Variable |
|
| Annotation Location Variable |
|
| Annotation Merge Variables |
|
| Annotation Plotting Group Variable |
|
| Annotation Position Variable |
|
| Annotation SAS Data Set |
|
| Apply a Shifted log2 Transformation for QC Analysis |
|
| Association Tests |
|
| Automated Linkage Group Clustering Method |
|
| Bandwidth |
|
| Beta value for Beta distribution |
|
| Binary Trait Variable |
|
| Binary Trait Variables |
|
| Break linkage groups based on: |
|
| Break linkage groups between markers with large ordered distances |
|
| By Variables |
|
| Calculate trend odds ratios |
|
| Categorical Variables |
|
| Categorical Variables Defining Groups |
|
| Categorical Variables for Model |
|
| Cells with Maximum Features Detected |
|
| Cells with Minimum Features Detected |
|
| Censor Values |
|
| Censor Variable |
|
| Center columns |
|
| Center rows |
|
| Change Output Folder to Workflow Folder in settings moved to right panel |
|
| Chromosome Variable |
|
| Cluster Significant Results |
|
| Clustering Method |
|
| Collapse rare variants within analysis group |
|
| Color Theme |
|
| Color Variable |
|
| Color Variable Type |
|
| Color Variables |
|
| Compress the K matrix |
|
| Compression Rate |
|
| Compute Q Variables from PCA |
|
| Compute results for annotated rows only |
|
| Compute results for exon annotated rows only |
|
| Compute sandwich (empirical) estimator of covariance matrix |
|
| Control Levels for Difference Comparisons |
|
| Control Levels for Differential Expression Comparisons |
|
| Conversion for P-Values |
|
| Correlation and Grouped Scatterplots |
|
| Correlation and Principal Variance Components Analysis |
|
| Create add-in package |
|
| Cross Type |
|
| Cumulative Proportion of Variation to Explain with Principal Components |
|
| Current Study |
|
| Data Set of Differences to Include from Comparison Set |
|
| Define linkage groups based on the: |
|
| Delete rows: |
|
| Delete rows with Interquartile Range satisfying this expression |
|
| Delete rows with Mean satisfying this expression |
|
| Delete rows with Median satisfying this expression |
|
| Delete rows with Number of Missing Values satisfying this expression |
|
| Delete rows with Percentile satisfying this expression |
|
| Delete rows with Standard Deviation satisfying this expression |
|
| Denominator Degrees of Freedom Method |
|
| Direction of the Cutoff |
|
| Direction of the Fold Change Cutoff |
|
| Direction of the Mean Difference Cutoff |
|
| Display marker genotype cell color plots |
|
| Display principal components plots |
|
| Distribution Analysis |
|
| Estimate LSMeans for these Fixed Effects |
|
| Event Trait Value |
|
| Exon (Probeset) ID Variable |
|
| Exon Annotation Chromosome Variable |
|
| Exon Annotation Label Variable |
|
| Exon Annotation Merge Variables |
|
| Exon Annotation Position Variable |
|
| Exon Annotation SAS Data Set |
|
| Exon Annotation Transcript Variable |
|
| Expected Segregation Ratios for AA AB BB |
|
| Experimental Design SAS Data Set |
|
| Features Detected in Minimum Cells |
|
| File Containing Estimate Statements |
|
| Filter Data with Zero or Missing Values |
|
| Filter Rows Whose Proportion of Zero/Missing Values Exceeds this Cutoff |
|
| Filter to Include Data in Analysis |
|
| Filter to Include Exon Annotation Rows for ANOVA |
|
| Filter to Include Individuals |
|
| Filter to Include Markers |
|
| Filter to Include miRNA Annotation Rows |
|
| Filter to Include Observations |
|
| Filter to Include Transcript Annotation Rows for ANOVA |
|
| Filter to Select Markers for Computing the K Matrix |
|
| Filter to Select Markers for PCA |
|
| Fix covariance parameters |
|
| Fixed Effects for Differential Expression |
|
| Fixed Effect Interactions with Exon ID Variable (Alternative Splicing) |
|
| Fold Change Filter Cutoff |
|
| Folder of Available Processes |
|
| Folder of Available Settings |
|
| Folder of Track Settings Files |
|
| Format of Marker Variables |
|
| Framework Linkage Group Variable |
|
| Framework Map Data Set |
|
| Framework Marker Name Variable |
|
| Framework Order Variable |
|
| GenBank Accession Variable |
|
| Gene Description Variable |
|
| Gene ID Variable |
|
| Gene Length Variable |
|
| Gene Symbol Variable |
|
| Genes of Interest |
|
| Genetic Distance Break Value |
|
| Genotype Delimiter |
|
| Genotyping Generation (n) |
|
| Group Percentage for Deletion |
|
| Grouping Method |
|
| Grouping Recombination Fraction Threshold |
|
| Hierarchical Clustering |
|
| Hotelling’s T-squared Test |
|
| ID Variables |
|
| Include 3D plots |
|
| Include adjusted p-values in addition to -log10(p-values) |
|
| Include Fold Changes in Addition to log Fold Changes |
|
| Include fold changes in addition to log2 fold changes |
|
| Include p-values in addition to -log10(p-values) |
|
| Individuals Minimum Proportion of Nonmissing Genotypes |
|
| Input data is log-transformed |
|
| Input Genotype SAS Data Set |
|
| Input SAS Data Set |
|
| Intensity Columns to Filter |
|
| Interaction Effects |
|
| JMP Journal Output File |
|
| K-Means Clustering |
|
| Kernel Function |
|
| Label Variable |
|
| Launch ANOVA for Differential Expression Analysis |
|
| Launch ANOVA Interface |
|
| List every model fit |
|
| List-Style Specification of Intensity Columns to Filter |
|
| List-Style Specification of Marker Variables |
|
| List-Style Specification of Trait Variables |
|
| List-Style Specification of Variables Whose Rows are to be Clustered |
|
| -log10(p-value) Cutoff |
|
| MAF Threshold for Rare Variants |
|
| Map Function |
|
| Marker Name Variable |
|
| Marker Variables |
|
| Max Iteration of t-SNE |
|
| Maximum Dimension of K Matrix |
|
| Maximum Dispersion to Filter Genes |
|
| Maximum Mean to Filter Genes |
|
| Maximum Number of Chromosomes Per Row in 3D Display |
|
| Maximum Number of Clusters for K-Means |
|
| Maximum Number of Principal Components |
|
| Maximum Number of Principal Components to Model |
|
| Mean Difference Filter Cutoff |
|
| Method |
|
| Minimum Dimension of K Matrix |
|
| Minimum Dispersion to Filter Genes |
|
| Minimum Distance of UMAP |
|
| Minimum Mean to Filter Genes |
|
| Minimum Number of Clusters for K-Means |
|
| Minimum Number of Observations Required for a Branch |
|
| Minimum Proportion of Nonmissing Genotypes |
|
| Minimum X Chromosome Heterozygosity for Females |
|
| Minor allele frequency at Marker Locus |
|
| Minor Allele Frequency Threshold |
|
| Minor Allele Frequency Threshold for Including SNPs |
|
| miRNA ID Variable |
|
| Model Data As: |
|
| Model interactions of these Fixed Effects with the Exon ID Variable (Screen for possible alternative splicing) |
|
| Modeling Distribution |
|
| Multiple-Locus Regression Model |
|
| Multiple-Locus Radial Basis Machine (Kernel Method) |
|
| Multiple Testing Correction |
|
| Multiple Testing Method |
|
| Multiple Testing Method for Segregation Tests |
|
| Normalization Method |
|
| Number of Clusters |
|
| Number of Clusters Expected |
|
| Number of Epochs of UMAP |
|
| Number of Linkage Groups |
|
| Number of Markers in Each Group |
|
| Number of Neighbors of UMAP |
|
| Number of Principal Components |
|
| Number of Principal Components to Use |
|
| Number of Rows in Input Data for Testing Run |
|
| Number of SNPs to Test |
|
| Number of the First Principal Component to Model |
|
| Number of Variable Genes to Keep |
|
| Organism |
|
| Output Data Set |
|
| Output Data Set Containing Filtered Data |
|
| Output Dimension of Embedding |
|
| Output File Prefix |
|
| Output Folder |
|
| Output genotype LS means and diffs |
|
| Output residuals from every model |
|
| P-Value Adjustment |
|
| p-Value Cutoff for Plots |
|
| p-Value Cutoff for Segregation Test Plots |
|
| PARMS Statement Values and/or Options |
|
| PC Regression Model |
|
| Pedigree ID |
|
| Percentage of Mitochondria Genes Allowed |
|
| Percentile to Compute for PCTL Statistic |
|
| Perform Case-Control Association Tests |
|
| Perform Missing Genotype by Trait Analysis |
|
| Perform multiallelic analysis on multiallelic markers |
|
| Perform shifted log2 transformation: |
|
| Perplexity of t-SNE |
|
| Plot Markers with significant p-values only |
|
| Position Variable |
|
| Prefix of Marker Variables |
|
| Principal Component Analysis |
|
| Principal Variance Component Effects for QC |
|
| PROC GLIMMIX Estimation Method |
|
| Random Effects |
|
| Random Mating Generation (t) Prior to Inbreeding |
|
| Random Statement Options |
|
| Recode genotypes numerically (2,1,0) |
|
| Recombination Fraction Break Value |
|
| Recombination Fraction Cutoff |
|
| Reference Trait Value |
|
| Remove Mitochondrial Genes from Analysis |
|
| Remove Ribosomal Genes from Analysis |
|
| Replace Cluster Means with representative observations |
|
| Replace highest values |
|
| Replace intensities falling above this column percentile |
|
| Replace intensities falling above this value |
|
| Replace intensities falling at least this many standard deviations above the column mean |
|
| Replace intensities falling at least this many standard deviations below the column mean |
|
| Replace intensities falling below this column percentile |
|
| Replace intensities falling below this value |
|
| Replace lowest values |
|
| Report SNP x Interaction Effect tests only |
|
| Results to Include in the Review |
|
| Review Output File |
|
| Run Analyses Above... |
|
| Run QC analyses: |
|
| Run Subset and Reorder Genetic Data process to order marker data for QTL analysis |
|
| Run t-SNE and UMAP (Appropriate R Packages Required) |
|
| Scale columns |
|
| Scale rows |
|
| Select Comparison Set for Differential Expression Tests |
|
| Select Comparison Set for Mean Differences Tests |
|
| Select Method |
|
| Separate and journal results by chromosome |
|
| Sequence Kernel Association Test (SKAT) |
|
| Server Output Directory |
|
| Shifted log2 Transformation for ANOVA |
|
| Shifted log2 Transformation for QC |
|
| Shifting Factor |
|
| Shifting Factor of log2 Transform for QC |
|
| Shifting Factor of log2 Transform before Normalization or ANOVA |
|
| Show Only: |
|
| Single-Locus Genotype Tests Pearson chi-square and Fisher’s exact |
|
| Single-Locus Regression Model |
|
| SNP ID Variable |
|
| SNPs: Minimum HWE p-Value |
|
| SNPs Minimum Minor Allele Frequency |
|
| SNPs Minimum Missing Genotype by Trait p-Value |
|
| SNPs Minimum Proportion of Nonmissing Genotypes |
|
| Sort settings by: |
|
| Strata Variables |
|
| Study |
|
| Study Name |
|
| Study Output Folder |
|
| Tau Value for TPM |
|
| Template Study |
|
| Template Study Output Folder |
|
| Terminate further processes when an error occurs |
|
| Test on a subset of SNPs |
|
| Track Settings Files |
|
| Trait Value of Individuals to Include in HWE Test |
|
| Trait Variables |
|
| Transcript Annotation Chromosome Variable |
|
| Transcript Annotation Label Variable |
|
| Transcript Annotation Merge Variables |
|
| Transcript Annotation Position Variable |
|
| Transcript Annotation SAS Data Set |
|
| Transcript Annotation Variables to Keep |
|
| Transcript Cluster ID Variable |
|
| Two Way Clustering |
|
| Type of Trait |
|
| Use lower boundary constraint of 0 for K matrix covariance parameter |
|
| Use QTL data numeric coding from JMP Genomics versions prior to 5.1 |
|
| Value Ordering for Nominal Color Variable |
|
| Value to Use to Replace Highest Values |
|
| Value to Use to Replace Lowest Values |
|
| Variable Containing Names of Marker Variables |
|
| Variable Gene Selection Method |
|
| Variables By Which to Merge Exon Annotation Data |
|
| Variables By Which to Merge Tx Annotation Data |
|
| Variables Defining Blocks |
|
| Variables Defining Groups |
|
| Variables for QC Plotting Groups |
|
| Variables to Keep in Linkage Map Data Set |
|
| Variables to Keep in Output |
|
| Variables to Retain in Linkage Map Data Set |
|
| Variables Whose Rows are to be Clustered |
|
| Variance Component Effects |
|
| Variant Weights |
|
| Where Clause for Subsetting Input Data Set in Test Run |
|
| Width of Positional Group |
|
| Workflow Folder |
|
| Workflow Output Name |
|
| Workflow to Journal |
|
| Workflow to Run |
|
| 1-D Test Step in cM (1-D Genomewide Scan) |
|
| 2-D Test Step in cM (2-D Genomewide Scan) |
|
| Absolute Mean Difference Cutoff for Continuous Predictors |
|
| Absolute Proportion Difference Cutoff for Class Predictors |
|
| Accession Number Variable |
|
| Add markers dropped out from marker reduction analysis back to the linkage groups |
|
| Additional Covariates |
|
| Additional Fixed Effects |
|
| Additional PROC CLUSTER Options |
|
| Additional PROC TREE Options |
|
| Additional Random Effects |
|
| Adjust permutation p-values for multiple testing |
|
| Affected Offspring Variables |
|
| Affected Sib-Pair Tests |
|
| Affected Value of Trait Variable |
|
| Algorithm |
|
| All markers are biallelic |
|
| Allele Characters for A (P1 line) and B (P2 line) |
|
| Allele Variables |
|
| Alpha |
|
| Alpha for Dprime Confidence Limits |
|
| Alpha for LSMeans Confidence Intervals |
|
| Alpha for Selecting PCs |
|
| Alpha Level for Covariates |
|
| Alpha Level for Empirical LOD Thresholds |
|
| Alpha value for Beta distribution |
|
| Annotation Accession Variable |
|
| Annotation Analysis Group Variable |
|
| Annotation Analysis Group Variable for Collapsing Rare Variants |
|
| Annotation By Group Variable |
|
| Annotation Group Variable |
|
| Annotation Input SAS Data Set |
|
| Annotation Label Variable |
|
| Annotation Location Variable |
|
| Annotation MAF Variable |
|
| Annotation Major Allele Variable |
|
| Annotation Minor Allele Variable |
|
| Annotation Plotting Group Variable |
|
| Annotation SAS Data Set |
|
| Annotation Variables to Drop |
|
| Annotation Variables to Keep |
|
| Annotation Weight Variable |
|
| Append markers dropped out from marker reduction analysis to the output data sets |
|
| Append prefix to current marker name |
|
| Apply adaptive weights |
|
| Apply mean-correction to covariates |
|
| Apply stopping rules for map order optimization |
|
| Apply VIF for genomic control |
|
| Association Tests |
|
| Assume Hardy-Weinberg equilibrium at all loci |
|
| Asymmetric Loss Fitting Proportion |
|
| Automated Linkage Group Clustering Method |
|
| Average Pool Size |
|
| Backcross Parental Lines Variable |
|
| Bandwidth |
|
| Base Input SAS Data Set |
|
| Beta value for Beta distribution |
|
| Binary Trait Variable |
|
| Binary Trait Variables |
|
| Block Partition Variable |
|
| Bootstrap Confidence Interval Alpha |
|
| Bootstrap Samples |
|
| Break linkage groups based on: |
|
| Break linkage groups between markers with large ordered distances |
|
| Build a Combined Wide Data Set |
|
| By Variables |
|
| Calculate allele odds ratios |
|
| Calculate trend odds ratios |
|
| Calculate p-values for F statistics |
|
| Categorical Covariates |
|
| Categorical Variables |
|
| Category Variable |
|
| Censor Limit (-log10 scale) |
|
| Censor Limit |
|
| Censor Values |
|
| Censor Variable |
|
| Censor Variables |
|
| Choose a linkage grouping method |
|
| Choose a method for RIL simulation |
|
| Choose the first-generation mating type |
|
| Choose the mating type |
|
| Choose the multi-generation mating type |
|
| Choose the selection direction |
|
| Choose the selection direction for the index |
|
| Choose the selection direction for the similarity |
|
| Choose the selection direction for the trait |
|
| Chromosome |
|
| Chromosome Label |
|
| Chromosome Label from Base Input SAS Data Set |
|
| Chromosome Number |
|
| Chromosome Variable |
|
| Cluster Center Variable |
|
| Cluster Variable |
|
| Cluster Variables |
|
| Clustering Method |
|
| Cofactor Categorical Variables |
|
| Cofactor Continuous Variables |
|
| Color of Bars ({r,g,b}) |
|
| Color Variable |
|
| Color Variable Type |
|
| Columns of Q Matrix sum to 1 |
|
| Columns of Q Matrix sum to 1 in Q1 Model |
|
| Columns of Q Matrix sum to 1 in Q2 Model |
|
| Columns of Q Matrix sum to 1 in Q3 Model |
|
| Compress output data set |
|
| Compression Method |
|
| Compression Rate |
|
| Compute Cholesky Root of Matrix |
|
| Compute sandwich (empirical) estimator of covariance matrix |
|
| Compute selection index |
|
| Compute the root of the matrix by SVD |
|
| Constrain negative IBD estimates to 0 |
|
| Continuous Covariates |
|
| Continuous Trait Variables |
|
| Control Marker Data Set - Sorted Marker List |
|
| Control Marker Number |
|
| Control Marker Selection Method |
|
| Convergence Criterion |
|
| Conversion for F Statistics p-Values |
|
| Conversion for p-Values |
|
| Correlation Radius for Clustering |
|
| Correlation Value for Clustering |
|
| Corresponding Key Chromosome Number Variable from Merge Input SAS Data Set (1-12) |
|
| Corresponding Key Grid Variable from Merge Input SAS Data Set (1-12) |
|
| Corresponding Key Marker Label from Merge Input SAS Data Set (1-12) |
|
| Corresponding Key Testing Location Variable from Merge Input SAS Data Set (1-12) |
|
| Create cell plot |
|
| Create data set containing haplotype frequency estimates |
|
| Create data set of covariance parameter estimates for every model fit |
|
| Create data set with numerically coded genotypes |
|
| Create data sets of CorrCoeff2 in matrix format |
|
| Create frequency charts |
|
| Create haplotype frequency charts |
|
| Create Hierarchical Cluster of SNPs |
|
| Create HTML output |
|
| Create merged PCA output data set |
|
| Create output data set containing allelic transmissions |
|
| Create Parallel Plot of SNPs |
|
| Create PARMS statement from optimal model covariance parameter estimates |
|
| Create Phase Assignment Data Set |
|
| Create SAS data set containing htSNP indicator variable |
|
| Create Significance Indicator Columns |
|
| Create Stability Point Plot |
|
| Create subset data set |
|
| Create tagSNP subset indicator variable |
|
| Criterion for Evaluating Sets of htSNPs |
|
| Criterion for Optimal Compression Level |
|
| Criterion for Stopping Model Selection |
|
| Cross Type |
|
| Cumulative Proportion of Variation to Explain with Principal Components |
|
| Current Value(s) Denoting Missing Genotypes or Alleles |
|
| Cutoff Level of Tree Axis |
|
| CV Partitioning Method |
|
| D’ between Marker and Disease Locus |
|
| Data Step Statements |
|
| Define linkage groups based on the: |
|
| Delete Nonmatching Rows |
|
| Delete Rows Not in Base Input SAS Data Set |
|
| Denominator Degrees of Freedom Method |
|
| Dependent Categorical Variable |
|
| Dependent Class Variable |
|
| Display cell plot of Mendelian errors |
|
| Display column attributes |
|
| Display marker genotype cell color plots |
|
| Display markers |
|
| Display principal components plots |
|
| Display QTL location |
|
| Distance to Include Downstream and Upstream of Gene |
|
| Distance Unit |
|
| Distance Unit for Defining Maximum Range of LD Blocks |
|
| Dprime Lower Confidence Limit greater than: |
|
| Dprime Upper Confidence Limit greater than: |
|
| Dprime Upper Confidence Limit less than: |
|
| Drop Alleles with frequency below: |
|
| Drop Last Allele for Each Marker |
|
| Effect Estimate or Direction Variable |
|
| Effect Estimate or Direction Variable is the odds ratio |
|
| EigenCore Multiple Testing Method |
|
| Environment Variables |
|
| Estimate Rho and K Rho |
|
| Estimate the Number of Founding Populations |
|
| Estimated Frequency Cutoff for Combining Rare Haplotypes |
|
| Estimation Method |
|
| Evaluate individuals in the Input SAS Data Set without making crosses |
|
| Event Trait Value |
|
| Exclude single-SNP genes |
|
| Expanded Genotype Recoding |
|
| Expected Segregation Ratios for AA AB BB |
|
| Extreme Sampling Percentile |
|
| Family Association Tests |
|
| Family Test Options |
|
| Feature Selection Criterion |
|
| File Filter Expression |
|
| Filter Defining First SNP in Interaction |
|
| Filter Defining Second SNP in Interaction |
|
| Filter to Include Annotation Rows |
|
| Filter to Include Linkage Groups |
|
| Filter to Include Markers |
|
| Filter to Include Markers (applies to both data sets) |
|
| Filter to Include Observations |
|
| Filter to Include Observations for HWE Test |
|
| Filter to Include Predictor Categorical Variables |
|
| Filter to Include Predictor Continuous Variables |
|
| Filter to Include Rows in Annotation SAS Data Set |
|
| Filter to Include Windows |
|
| Filter to Select Null SNPs |
|
| Filter to Specify Recurrent Parental Lines |
|
| Filter Variables |
|
| First Column to Display |
|
| First Row to Display |
|
| Fit Square Root of Recombination Fractions in MDS Algorithm |
|
| Fix covariance parameters |
|
| Fixed Threshold |
|
| Flip alleles for A/T or C/G SNPs with major/minor alleles reversed from reference |
|
| Folder Containing Scoring Code Files |
|
| Folder of Input SAS Data Sets |
|
| Folder of Linkage Map Files |
|
| Force all markers into linkage groups |
|
| Format of Marker Variables |
|
| Format of SNP Variables |
|
| Framework Linkage Group Variable |
|
| Framework Map Data Set |
|
| Framework Marker Name Variable |
|
| Framework Order Variable |
|
| Frequency Cutoff |
|
| Frequency Cutoff for Combining Haplotypes |
|
| Frequency Initialization |
|
| Frequency Variable |
|
| Function of Covariates |
|
| Function of Trait Variable |
|
| Gene By Variables |
|
| Gene Input SAS Data Set |
|
| Gene Label |
|
| Gene Start Variable |
|
| Gene Stop Variable |
|
| Genetic Distance Break Value |
|
| Genetic Distance Unit for Results Plots |
|
| Genotype Data Set |
|
| Genotype Delimiter |
|
| Genotype Probability Data Set |
|
| Genotype Probability Variables |
|
| Genotype Recoding |
|
| Genotype to code as 2 for the Trend Test |
|
| Genotype to code as 2 for the Trend Test ORs |
|
| Genotype Variable |
|
| Genotyping Generation (n) |
|
| Grouping LOD Score Threshold |
|
| Grouping LOD Threshold |
|
| Grouping Method |
|
| Grouping Recombination Fraction Threshold |
|
| Grouping Variable |
|
| Haplotype Estimation Method |
|
| Haplotype Frequency Data Set |
|
| Heat Map Color Theme |
|
| High-risk Allele Frequency |
|
| Hold L at starting value |
|
| Hold M at starting value |
|
| Hold-Out Method |
|
| Hold-Out Size, Specify as: |
|
| Hotelling’s T-squared Test |
|
| IBD Data Set |
|
| IBS sharing counted for: |
|
| ID Variables |
|
| Identity By Descent Threshold |
|
| Identity By State Threshold |
|
| Impute zeros for missing continuous predictor values |
|
| Impute zeros for missing values |
|
| Inbreeding Coefficient |
|
| Include 3D plots |
|
| Include direction of variant effect in test |
|
| Include framework markers in the K-Means clustering analysis |
|
| Include self crosses |
|
| Increase R Software memory limit |
|
| Increment |
|
| Individual ID |
|
| Individual ID Variable |
|
| Individuals to Include in Matrix |
|
| Initial Number of Linkage Groups |
|
| Input data contains means of genotypes on each environment |
|
| Input Linkage Map SAS Data Set |
|
| Input SAS Data Set |
|
| Input Genotype SAS Data Set |
|
| Input K Matrix Data Set |
|
| Interaction Block Variables |
|
| Interaction Effects |
|
| Interactive Clustering Method |
|
| Interactive Linkage Group Clustering Method |
|
| Italics Value |
|
| Italics Variable |
|
| JMP Script Output File Name |
|
| K for K-Fold CV |
|
| K for K-Fold or 1/K Hold-Out |
|
| K Matrix is compressed |
|
| K Matrix is compressed in K1 Model |
|
| K Matrix is compressed in K2 Model |
|
| K Matrix Square Root Variables |
|
| K Matrix Square Root Variables in K1 Model |
|
| K Matrix Square Root Variables in K2 Model |
|
| K-Means Clustering Method |
|
| Keep original marker variables |
|
| Kernel Function |
|
| Key Chromosome Number Variable from Base Input SAS Data Set |
|
| Key Chromosome Variable from Base Input SAS Data Set |
|
| Key Grid Variable from Base Input SAS Data Set |
|
| Key Marker Label from Base Input SAS Data Set |
|
| Key Testing Location Variable from Base Input SAS Data Set |
|
| Kinship Matrix Diagonal |
|
| Krho |
|
| L for Leave-L-Out |
|
| Label Variable |
|
| Linear-Bilinear Model |
|
| Linkage Group Hierarchical Clustering Method |
|
| Linkage Group Variable |
|
| Linkage Group Variable 1 |
|
| Linkage Group Variable 2 |
|
| Linkage Map Files |
|
| Linkage Map Weight List |
|
| Linkage Phase Data Set |
|
| Linkage Phase of Adjacent Markers |
|
| List every model fit |
|
| List of number of simulated progenies |
|
| List of optimization direction (one value per trait) |
|
| List of percent cut off (one value per generation) |
|
| List of selection index cutoff (one value per generation) |
|
| List of selection similarity cut off (one value per generation) |
|
| List of threshold direction (one value per trait) |
|
| List of threshold values (one value per trait) |
|
| List of weight values for the selection index |
|
| List-Style Specification of K Matrix Square Root Variables |
|
| List-Style Specification of K Matrix Square Root Variables in K1 Model |
|
| List-Style Specification of K Matrix Square Root Variables in K2 Model |
|
| List-Style Specification of LOD Score Variables |
|
| List-Style Specification of Marker Variables |
|
| List-Style Specification of Matrix Variables |
|
| List-Style Specification of Numeric SNP Variables |
|
| List-Style Specification of Predictor Categorical Variables |
|
| List-Style Specification of Predictor Continuous Variables |
|
| List-Style Specification of Q Matrix Variables |
|
| List-Style Specification of Q Matrix Variables in Q1 Model |
|
| List-Style Specification of Q Matrix Variables in Q2 Model |
|
| List-Style Specification of Q Matrix Variables in Q3 Model |
|
| List-Style Specification of Recombination Rate Variables |
|
| List-Style Specification of SNP Variables |
|
| List-Style Specification of SNP Variables to Keep in Output Data Set |
|
| List-Style Specification of SNP Variables to Retain in Output Data Set |
|
| List-Style Specification of Trait Variables |
|
| List-Style Specification of Variables to Be Standardized |
|
| List-Style Specification of Variables to Keep in Output Data Set |
|
| List-Style Specification of Variables to Retain in Output Data Set |
|
| Listing for Each Model Fit |
|
| Location Variable |
|
| LOD Score Break Value |
|
| LOD Score ID Variable |
|
| LOD Score SAS Data Set |
|
| LOD Score Variables |
|
| LOD Threshold [1,10] |
|
| LOD Threshold for Entry into the MIM Model |
|
| LOD Threshold for Staying in the MIM Model |
|
| -log10(p-Value) Cutoff |
|
| log10 Regularization Parameter |
|
| MAF Threshold for Rare Variants |
|
| Main Test Step in cM |
|
| Major Allele Variable |
|
| MANOVA Statistic |
|
| Map Function |
|
| Map 1 Label |
|
| Map 2 Label |
|
| Marker 1 Label |
|
| Marker 2 Label |
|
| Marker 1 Location |
|
| Marker 2 Location |
|
| Marker Genotype Variables |
|
| Marker ID Variable |
|
| Marker ID Merge Variable |
|
| Marker Label |
|
| Marker Location Unit |
|
| Marker locus is disease locus |
|
| Marker Name Variable |
|
| Marker Name Variable 1 |
|
| Marker Name Variable 2 |
|
| Marker Names Variable |
|
| Marker Order Variable |
|
| Marker Physical Position |
|
| Marker Position |
|
| Marker Type |
|
| Marker Variables |
|
| Maternal Value of the Sex Variable |
|
| Matrix Variables |
|
| Max Number of Categories Allowed in a Predictor |
|
| Max Number of Effects in the Model |
|
| Max Number of Variables to Consider for Splitting a Node |
|
| Maximum |
|
| Maximum Convergency Tolerance |
|
| Maximum Dimension of K Matrix |
|
| Maximum Depth of Tree |
|
| Maximum Distance |
|
| Maximum Interval Window List |
|
| Maximum Iterations |
|
| Maximum Number of Chromosomes Per Row in 3D Display |
|
| Maximum Number of Clusters |
|
| Maximum Number of Filtered Predictors |
|
| Maximum Number of Iterations |
|
| Maximum Number of Intervals to Fit Together as a Region |
|
| Maximum Number of K-Means Clusters / Predictors |
|
| Maximum Number of Principal Components |
|
| Maximum Number of Steps |
|
| Maximum Number of Trees |
|
| Maximum Number of Variables to Select with Model Averaging |
|
| Maximum Number of Variables to Select with Pooling |
|
| Maximum Order of Interactions |
|
| Maximum Range of LD Blocks |
|
| Maximum Recombination Fraction Threshold |
|
| Maximum Subset Size |
|
| Maximum Time per Algorithm Iteration (in minutes) |
|
| Maximum X Chromosome Heterozygosity for Males |
|
| Mean Square Blocks or Replicates within Environments |
|
| Mean Square Environment |
|
| Mean Square Error |
|
| Mean Square Error Degrees of Freedom |
|
| Measure for LD Contour Plot |
|
| Measure for LD Decay Plot |
|
| Measure of Genetic Distance |
|
| Merge Individual ID Variable |
|
| Merge Input SAS Data Set (1-12) |
|
| Merge Key Variables |
|
| Method to Order Populations |
|
| Method to Use |
|
| Minimum |
|
| Minimum Dimension of K Matrix |
|
| Minimum LOD Threshold |
|
| Minimum Number of Linkage Groups |
|
| Minimum Number of Observations Required for a Branch |
|
| Minimum Number of Offspring Sharing for Computing Runs |
|
| Minimum Proportion of Nonmissing Genotypes |
|
| Minimum Run Length for Including in Output |
|
| Minimum X Chromosome Heterozygosity for Females |
|
| Minor Allele Frequency at Marker Locus |
|
| Minor Allele Frequency Threshold |
|
| Minor Allele Frequency Threshold for Including SNPs |
|
| Model Selection Method |
|
| Multi-Marker Model Selection |
|
| Multiple-Locus Regression Model |
|
| Multiple Testing Correction |
|
| Multiple Testing Method |
|
| Multiple Testing Method for Segregation Tests |
|
| Nearby Marker Recombination Constraint |
|
| Nominalize Continuous Dependent Variables |
|
| Null SNP Variables |
|
| Number of Backcross Generations |
|
| Number of Clusters |
|
| Number of Clusters for Automated Compression |
|
| Number of Columns |
|
| Number of Contours |
|
| Number of Distinct Genotypes |
|
| Number of Generations |
|
| Nearby LOD Score Constraint |
|
| Number of Founding Populations |
|
| Number of Intervals to Overlap in Consecutive Regions |
|
| Number of Legend Decimals |
|
| Number of Legend Levels |
|
| Number of Linkage Groups |
|
| Number of Markers in Each Group |
|
| Number of model averaging samples |
|
| Number of Permutations |
|
| Number of Permutations or Simulations to Perform |
|
| Number of Permutations to Compute |
|
| Number of Permutations to Perform |
|
| Number of Principal Components |
|
| Number of Random Hold-Out Iterations |
|
| Number of Reconfigurations |
|
| Number of Representative Markers |
|
| Number of Rounds of Selection |
|
| Number of Rows |
|
| Number of Selections to Display |
|
| Number of Selfing Generations |
|
| Number of Shuffles |
|
| Number of Simulated Progeny for Each Cross |
|
| Number of Simulations for MAX Test |
|
| Number of Starts |
|
| Number of Steps |
|
| Number of Variables to Process at a Time |
|
| Numeric Marker Variables |
|
| Numeric SNP Variables |
|
| Numerical Parameter for Advanced Standardization Methods |
|
| Observed Frequency Cutoff for Dropping Rare Haplotypes |
|
| Optimize the continuous predictor set |
|
| Optimized Automated Clustering Method |
|
| Options to Define Cluster Membership |
|
| Order Algorithm |
|
| Order Data Set |
|
| Other Accession Number Variables |
|
| Other Chromosome Variables |
|
| Other Effect Estimate Variables |
|
| Other Location Variables |
|
| Other Major Allele Variables |
|
| Other p-Value Variables |
|
| Other Sample Size Variables |
|
| Other SNP ID Variables |
|
| Other Standard Error Variables |
|
| Other Variables to Keep in Output Data Set |
|
| Other Variables to Retain in Output Data Set |
|
| Output Annotation Data Set |
|
| Output covariance parameter estimates from every model |
|
| Output Data Set |
|
| Output Data Set Prefix |
|
| Output File Name |
|
| Output File Prefix |
|
| Output fitness statistics for every model |
|
| Output Folder |
|
| Output Genotype Data Set |
|
| Output genotype LS means |
|
| Output genotype LS means and diffs |
|
| Output M and L Data Set |
|
| Output Map Data Set |
|
| Output markers with significant p-values only |
|
| Output most probable haplotype pair only |
|
| Output parameter estimates from every model |
|
| Output predicted values from every model |
|
| Output R-Square from the logistic regression of binary, nominal, and ordinal traits |
|
| Output residuals from every model |
|
| Output SAS data set of between and within family component variables for the O-QTDT |
|
| Output simulated progenies data set |
|
| Output survival function estimates for viewing survival curves |
|
| P for P-Percent-Hold-Out |
|
| p-Value Adjustment |
|
| p-Value Combination Method |
|
| p-Value Cutoff for Segregation Test Plots |
|
| p-Value Variable |
|
| Parent 1 ID |
|
| Parent 2 ID |
|
| Parent Variables |
|
| PARMS Statement Values and/or Options |
|
| PC Regression Model |
|
| PCA Data Set |
|
| Pedigree Data Set |
|
| Pedigree ID |
|
| Pedigree ID Variable |
|
| Pedigree ID Variable in K1 Model |
|
| Pedigree ID Variable in K2 Model |
|
| Percent Cut Off |
|
| Perform 2-sided Test |
|
| Perform association tests on selected markers |
|
| Perform association tests on unselected markers conditional on selected markers |
|
| Perform EigenCorr to select PCs |
|
| Perform F statistics calculations |
|
| Perform genetic distance matrix calculations |
|
| Perform LD calculations for all pairs within annotation groups |
|
| Perform model averaging |
|
| Perform poolwise selection |
|
| Perform Principal Components Analysis |
|
| Perform recoding with respect to the: |
|
| Perform SAS-based clustering on the genetic distance matrix |
|
| Permutations |
|
| Phase Assignment ID Variables |
|
| Phase Assignment Probability Cutoff |
|
| Phased Haplotypes Data Set |
|
| Phenotyping Generation (m) |
|
| Ploidy Number |
|
| Plot haplotypes with significant p-values only |
|
| Plot heatmaps for linkage groups |
|
| Plot Markers with significant p-values only |
|
| Plot Markers with significant F ST p-values only |
|
| Plot Relationship Matrix heat map |
|
| Population Prevalence |
|
| Population Variable |
|
| Position Variable |
|
| Position Variable 1 |
|
| Position Variable 2 |
|
| Power Values |
|
| Predictor Categorical Variables |
|
| Predictor Continuous Variables |
|
| Prefix |
|
| Prefix for Column Names of Expanded Genotypes |
|
| Prefix for Column Names of Recoded Genotypes |
|
| Prefix for Naming Distance Output Variables |
|
| Prefix for Naming Output Variables |
|
| Preliminary Delimiter Separating Annotation Categories (Enclose in Quotes) |
|
| Prior Probabilities / Prevalences |
|
| PROC GENESELECT Statement Options |
|
| PROC GLIMMIX Estimation Method |
|
| PROC MIXED Estimation Method |
|
| Proportion of Alleles Identical by State Threshold |
|
| Proportion of Informative Pairs in Strong LD greater than: |
|
| Q and K Data Set |
|
| Q Matrix Variables |
|
| Q Matrix Variables in Q1 Model |
|
| Q Matrix Variables in Q2 Model |
|
| Q Matrix Variables in Q3 Model |
|
| QTDT Tests |
|
| QTL Effect Size Variables from Base Input SAS Data Set |
|
| QTL Effect Size Variables from Merge Input SAS Data Set (1-12) |
|
| QTL Indicator Variable from Base Input SAS Data Set |
|
| QTL Indicator Variable from Merge Input SAS Data Set (1-12) |
|
| QTL Mapping Method |
|
| QTL Mapping Model Algorithm |
|
| QTL Test Size Variables from Base Input SAS Data Set |
|
| QTL Test Size Variables from Merge Input SAS Data Set (1-12) |
|
| QTL Test Step in cM |
|
| Quantile Level |
|
| Quantitative Trait Variables |
|
| Quantitative Variables |
|
| R Software Memory Size (Mb) |
|
| R-squared Threshold |
|
| Radial Basis Machine (Kernel Method) |
|
| Random Effects |
|
| Random Mating Generation (t) Prior to Inbreeding |
|
| Random Number Seed |
|
| Random Number Seed for Forest |
|
| Random Number Seed for Testing F Statistics |
|
| Random Statement Options |
|
| Range of Markers Variable |
|
| Rare Variant Recoding |
|
| RATE= Option |
|
| Recombination Fraction Break Value |
|
| Recombination Fraction Cutoff |
|
| Proximity to Optimal Mapping Order |
|
| Recombination Rate Variables |
|
| Reference Annotation SAS Data Set |
|
| Reference Annotation Label Variable |
|
| Reference Annotation Major Allele Variable |
|
| Reference Annotation Minor Allele Variable |
|
| Reference Population for FST |
|
| Reference Trait Value |
|
| Relationship Matrix to Compute |
|
| Risk of Observing the Trait in the Heterozygous Genotype (A/a) Relative to the Homozygous Recessive Genotype (a/a) |
|
| Risk of Observing the Trait in the Homozygous Dominant Genotype (A/A) Relative to the Homozygous Recessive Genotype (a/a) |
|
| Remove markers not found in Annotation SAS Data Set |
|
| Reorder Variables |
|
| Replicate Variable |
|
| Report SNP x Interaction Effect tests only |
|
| Reverse Color Theme |
|
| Rho |
|
| Sample Proportion of Cases |
|
| Sample Size Variable |
|
| Sample Sizes |
|
| SAS Data Set Indicating Which Crosses to Simulate |
|
| SAS Data Sets |
|
| Save Data Set for Each Window |
|
| Scoring Code Files |
|
| Search Method |
|
| Select best simulated progenies based on trait values |
|
| Select simulated progenies based on similarity to parents |
|
| Selection Criterion for Main Effect Search and Drop |
|
| Selection Criterion for Interaction Search and Drop |
|
| Selection Index Cut Off |
|
| Sequence Kernel Association Test (SKAT) |
|
| Server Output Directory |
|
| Sex Variable |
|
| Shuffle Markers |
|
| Shuffling LOD Threshold |
|
| Shuffling Window Size |
|
| Significance Level for Entry into the MIM Model |
|
| Significance Level for Entry into the Model |
|
| Significance Level for Staying in the MIM Model |
|
| Significance Level for Staying in the Model |
|
| Similarity Measure |
|
| Simulate data from all crosses |
|
| Simulate multiple generations |
|
| Simulate progenies |
|
| Simulate RIL progenies |
|
| SL for Adding Variables |
|
| SL for Keeping Variables |
|
| SL for Keeping Variables in the Selected Model |
|
| Sliding Window Size |
|
| Sliding Window Variable |
|
| SNP Data Set |
|
| SNP ID Variable |
|
| SNP Variables |
|
| SNP Variables (Coded Numerically) |
|
| SNP Variables to Keep in Output Data Set |
|
| SNP Variables to Retain in Output Data Set |
|
| Specification of Regularization Parameter (Lambda) |
|
| Standard Error Estimate |
|
| Standard Error Variable |
|
| Standardize genotypes |
|
| Standardize Predictors Row-Wise |
|
| Standardization Method for Predictor Continuous Variables |
|
| Starting Value for E, the Exponential Decline of Rho with Physical Distance |
|
| Starting Value for L, the Bias at Large Distance |
|
| Starting Value for M, the Proportion of the Youngest Haplotype that is Monophyletic |
|
| Statistical Testing Method for Continuous Predictors |
|
| Stepwise EM Cutoff |
|
| Strata Variable |
|
| Strata Variables |
|
| Study |
|
| Subset Size |
|
| Suppress all graphical and HTML output |
|
| Tau Value for TPM |
|
| Temperature |
|
| Temperature Reduction Factor |
|
| Test allelic association for LD |
|
| Test Data Set |
|
| Test each marker individually |
|
| Test for HWE |
|
| Test Individual Haplotypes |
|
| Test Statistic |
|
| Test Window Size in cM |
|
| Tests |
|
| Top Cross Tester Lines Indicator Variable |
|
| TOTAL= Option |
|
| Trait Variable |
|
| Trait Variables |
|
| Transformation of Input p-Values |
|
| Transformation of Output p-Values |
|
| Transformation for Predictor Continuous Variables |
|
| Transpose data for cell plot |
|
| Treat missing genotypes as: |
|
| Type I Error Rate |
|
| Type of Coefficients to Calculate |
|
| Type of Kernel to Use |
|
| Type of Model |
|
| Type of Tests to Perform |
|
| Type of Trait |
|
| Type of Weight to Use |
|
| Usage of K-Means Clusters |
|
| Use a variable threshold for including variants |
|
| Use Annotation Label Variable for Variable Prefixes |
|
| Use Automated Hierarchical Clustering to Assign Linkage Groups |
|
| Use bias corrected recombination formula for RIL |
|
| Use dominant coding for trend test |
|
| Use Forest to create interaction indicators |
|
| Use Forest to filter predictors |
|
| Use genetic map to simulate linkage |
|
| Use grid computing |
|
| Use K-Means clustering to reduce marker number |
|
| Use K-Means clustering to reduce number of markers |
|
| Use K-Means clustering to reduce predictors |
|
| Use lower boundary constraint of 0 for K matrix covariance parameter |
|
| Use Monte Carlo simulations for KBAC p-values |
|
| Use QTL data numeric coding from JMP Genomics versions prior to 5.1 |
|
| Use rank-based statistic for tests |
|
| Use reported value of sex variable for genetic sex when ambiguous |
|
| Use statistical testing to filter predictors |
|
| Value of the Backcross Parental Lines Variable Indicating the Parental Line 1 |
|
| Value of the Backcross Parental Lines Variable Indicating the Parental Line 2 |
|
| Value Ordering for Nominal Color Variable |
|
| Value Ordering for Nominal Variables |
|
| Value Representing Cases |
|
| Value to Impute for Missing Genotypes |
|
| Variable By Which to Merge Annotation Data |
|
| Variable Containing Names of Marker Variables |
|
| Variable to Define Tree Axis |
|
| Variables to Be Standardized |
|
| Variables to Drop |
|
| Variables to Keep in Linkage Map Data Set |
|
| Variables to Keep in Output Data Set |
|
| Variables to Keep in PCA Data Set |
|
| Variables to Retain in Linkage Map Data Set |
|
| Variables to Retain in Output Data Set |
|
| Variant Weights |
|
| Weight the MDS Fit Based on Recombination Fractions |
|
| Weight Variable |
|
| Weighting Method for Sibships |
|
| Width of Positional Group |
|
| Window Overlap |
|
| Window Size in cM |
|
| Window Size Unit |
|
| X-linked Marker Clause |
|
| X-linked Markers Clause |
|
| X-linked Markers Clause |
|
| Add Mean Difference filter to select significant tests |
|
| Additional Bandwidth on Each Side of Tracks |
|
| Adjustment Effects |
|
| Alpha |
|
| Annotation Chromosome Variable |
|
| Annotation Label Variable |
|
| Annotation Merge Variables |
|
| Annotation Position Variable |
|
| Annotation SAS Data Set |
|
| Annotation Variables to Keep |
|
| Annotation Variables to Keep in Output Data Set |
|
| Annotation Variables to Retain in Output Data Set |
|
| Bin Method |
|
| Bin Summary Statistic |
|
| By Variables |
|
| Calculate the absolute value of the differences |
|
| Categorical Variables |
|
| Categorical Variables Defining Groups |
|
| Center rows |
|
| Chromosome Variable |
|
| Cluster significant Mean profiles |
|
| Cluster Significant Results |
|
| Color Theme |
|
| Color Variables |
|
| Compute Pearson covariances instead of correlations |
|
| Compute results for annotated rows only |
|
| Control Levels |
|
| Control Levels for Difference Comparisons |
|
| Control Reference Value |
|
| Control Set Summary Statistic |
|
| Cumulative Proportion of Variation to Explain |
|
| Data Set to Use for Filter |
|
| Density Smoothing Bandwidth Computation Method |
|
| Density Smoothing Bandwidth Multiplier |
|
| Direction of the Cutoff |
|
| Display detailed distribution statistics and histograms |
|
| Display Format for Density Grid Points |
|
| Display side-by-side box plots |
|
| Display Standard Deviation versus Mean plots |
|
| Exclude rows with missing physical position |
|
| Experimental Design SAS Data Set |
|
| Experimental Factor Variables |
|
| File Containing Estimate Statements |
|
| Filter to Include Annotation Rows |
|
| Filter to Include Observations |
|
| Filter to Include Rows |
|
| Folder of Track Settings Files |
|
| GenBank Accession Variable |
|
| Gene Description Variable |
|
| Gene Variable |
|
| Gene Symbol Variable |
|
| ID Variable |
|
| ID Variables to Keep |
|
| Include adjusted p-values in addition to -log10(p-values) |
|
| Include p-values in addition to -log10(p-values) |
|
| Include Standard Errors |
|
| Include t-Statistics |
|
| Input SAS Data Set |
|
| Intensity Variables to Bin |
|
| JMP Script Output file Name |
|
| JMP Script Output File Name |
|
| JSL Output File |
|
| K for Circular B S Minor Arc |
|
| Key Variable(s) to Merge with Input SAS Data Set |
|
| Label Variable |
|
| List every model fit |
|
| List-Style Specification of Intensity Variables to Bin |
|
| List-Style Specification of Variables |
|
| List-Style Specification of Variables for Which to Display Distributions |
|
| List-Style Specification of Variables to be Standardized |
|
| List-Style Specification of Variables to Partition Intensity Values |
|
| List-Style Specification of With Variables |
|
| -log(Alpha) for Stopping Rule |
|
| -log10(p-value) Cutoff |
|
| Maximum Depth of Recursion |
|
| Maximum Number of Principal Components to Apply |
|
| Mean Difference Filter Cutoff |
|
| Merge Annotation into Residuals Data Set |
|
| Merge Key Variables to Associate with Input SAS Data Set |
|
| Minimum Segment Size |
|
| Multiple Testing Method |
|
| Negative Mean Intensity Maximum [<=0] |
|
| Number of Density Grid Points |
|
| Number of Markers in Each Bin |
|
| Number of Permutations |
|
| Number of the First Principal Component for VCA |
|
| Numerical Parameter for Advanced Standardization Methods |
|
| Organism |
|
| Output Data Set |
|
| Output Eigenvalues Data Set |
|
| Output Experimental Design Data Set |
|
| Output Folder |
|
| Output experimental samples only |
|
| Output Prefix |
|
| Output Statistics Data Set |
|
| Output Test Data Set |
|
| Output Variance Components Data Set |
|
| Overlay density estimates |
|
| Perform log2 transform after standardization |
|
| Perform LOH targeted subtraction |
|
| Plot standardized residuals |
|
| Position Variable |
|
| Positive Mean Intensity Minimum [>=0] |
|
| Probe or SNP ID Variable |
|
| PROC GENESELECT Statement Options |
|
| Sample Set(s) to Use for Subtraction |
|
| Scale rows |
|
| Select Comparison Set for Mean Differences Tests |
|
| Separate and journal results by chromosome |
|
| Server Output Directory |
|
| Shifting Factor |
|
| Shrink variances using Empirical Bayes |
|
| SNP ID Variable |
|
| Standardization Method |
|
| Standardization Method for Comparing Means |
|
| Standardization Statistics Input SAS Data Set |
|
| Standardize |
|
| Standardized Residuals Output Data Set Name |
|
| Study |
|
| Subset Data Set to Use for Normalization |
|
| Track Settings Files |
|
| Type of Correlation |
|
| Uniformly scale histograms in detail plots |
|
| Uniformly scale y-axes in Volcano and Chromosome Position plots |
|
| Uniformly scale y-axes in Volcano plots |
|
| Variable Distinguishing Bivariate Observations |
|
| Variables |
|
| Variables By Which to Merge Annotation Data |
|
| Variables By Which to Merge Filter Data Set |
|
| Variables Defining Analysis Groups |
|
| Variables Defining Blocks |
|
| Variables Defining Control Sets |
|
| Variables Defining Groups for Mean Processing |
|
| Variables for Which to Display Distributions |
|
| Variables to Keep in Output |
|
| Variables to be Standardized |
|
| Variables to Partition Intensity Values |
|
| Variance Component Effects |
|
| Width of Positional Bin |
|
| With Variables |
|
| Alpha |
|
| Bandwidth |
|
| Between-Group Overlay Jitter |
|
| Bin Method |
|
| Bin Size |
|
| Bin Summary Statistic |
|
| Bin Width |
|
| By Variable |
|
| By Variables |
|
| Filter to Include Observations |
|
| ID Variables to Keep |
|
| Input SAS Data Set |
|
| JMP Script Output file Name |
|
| JMP Script Output File Name |
|
| Label Variable |
|
| List-Style Specification of y Variables |
|
| List-Style Specification of y Variables Group A |
|
| List-Style Specification of y Variables Group B |
|
| List-Style Specification of y Variables to Bin |
|
| List-Style Specification of y Variables to Detrend |
|
| log2 transform areas or heights |
|
| Lower and Upper x-Axis Values for Noise Intervals |
|
| Maximum Number of Peaks to Compute |
|
| Noise Baseline Fitting Option |
|
| Noise Cutoff |
|
| Output Data Set |
|
| Output Details Data Set |
|
| Output Folder |
|
| Peak Cutoff |
|
| Peak Quantity to Output |
|
| Percentage of Maximum Signal Below Which is Noise |
|
| Plot raw data |
|
| Response Density SAS Statements |
|
| Scale the area under the curve |
|
| Server Output Directory |
|
| Statistical Test |
|
| Study |
|
| Trim below zero |
|
| Trim Peak Maximum |
|
| Trim Valley Minimum |
|
| Within-Group Overlay Jitter |
|
| x Smoothing Bandwidth Multiplier |
|
| x Variable |
|
| x Variable Lower Bound |
|
| x Variable Number of Grid Points |
|
| x Variable Upper Bound |
|
| y Smoothing Bandwidth Multiplier |
|
| y Variable |
|
| y Variable Lower Bound |
|
| y Variable Number of Grid Points |
|
| y Variable Upper Bound |
|
| y Variables |
|
| y Variables to Bin |
|
| y Variables to Detrend |
|
| y Variables Group A |
|
| y Variables Group B |
|
| z Variable |
|
| z Variable Lower Bound |
|
| z Variable Upper Bound |
|
| z Variables |
|
| Accumulative Proportion of Variation |
|
| Add Mean Difference filter to select significant tests |
|
| Additional Bandwidth on Each Side of Tracks |
|
| Additional Covariates |
|
| Additional Fixed Effects |
|
| Additional PROC MIXED Statements |
|
| Adjust Counts by Total Counts |
|
| Adjustment Effects |
|
| Allele Variable |
|
| Alpha |
|
| Alpha Values |
|
| Annotation Chromosome Variable |
|
| Annotation Label Variable |
|
| Annotation Merge Variables |
|
| Annotation Merging Variable |
|
| Annotation Position Variable |
|
| Annotation SAS Data Set |
|
| Annotation Title Variables |
|
| Annotation Variables to Keep |
|
| Apply Certain Samples as Reference |
|
| Apply data from autosomes for normalization |
|
| Apply kernel density estimation for MA plot |
|
| Apply normalized data for MA plot |
|
| Apply reference baseline from previously input data set |
|
| Array Standardization Method |
|
| Apply weighting approach for trimmed mean |
|
| Array Variables to Plot |
|
| Bandwidth Multiplier of x-Dimension |
|
| Bandwidth Multiplier of y-Dimension |
|
| Baseline |
|
| Baseline in Reference SAS Data Set |
|
| Baseline Quantification |
|
| Baseline reference data is log-transformed |
|
| Baseline Reference SAS Data Set |
|
| Baseline Value |
|
| Baseline Variable |
|
| Batch Profile Input SAS Data Set |
|
| Biomaterial Provider |
|
| Block Variable |
|
| By Variable |
|
| By Variables |
|
| By Variables for Loess Normalization |
|
| Calculate the absolute value of the differences |
|
| Catalog Number |
|
| Categorical Variables |
|
| Categorical Variables Defining Groups |
|
| Cells with Maximum Features Detected |
|
| Cells with Minimum Features Detected |
|
| Censor Variable |
|
| Center rows |
|
| Characteristics |
|
| Chromosome Variable |
|
| Cluster significant Mean profiles |
|
| Cluster Significant Results |
|
| Coating |
|
| Color Scale |
|
| Color Variable |
|
| Color Variables |
|
| Column to Identify Control Rows in the EDDS |
|
| Columns by Which to Merge with Input SAS Data Set |
|
| Columns Defining Batches |
|
| Component Output Data Set Name |
|
| Compute Component Fixed-Effect Tests |
|
| Compute Multiple Testing Adjustment Separately for Each Test |
|
| Compute Pearson covariances instead of correlations |
|
| Compute results for annotated rows only |
|
| Compute results for secondary annotated rows only |
|
| Constants for Each Variance Component |
|
| Contributors |
|
| Constant to Apply |
|
| Control Levels |
|
| Control Set Design |
|
| Control Levels for Difference Comparisons |
|
| Control Levels for Differential Expression Comparisons |
|
| Control Set Summary Statistic |
|
| Coordinate Data Set |
|
| Coordinate Merge Variables |
|
| Covariates for Differential Expression |
|
| Create JMP Surface plot |
|
| Cumulative Proportion of Variation to Explain |
|
| Data Processing |
|
| Data Set of Differences to Include from Comparison Set |
|
| Data Set to Use for Filter |
|
| Delete nonmatching rows |
|
| Delete rows |
|
| Delete rows not in First Tall Data Set |
|
| Delete rows with at least this percentage of Missing values |
|
| Delete rows with Interquartile Range satisfying this expression (use keyword IQR) |
|
| Delete rows with Mean satisfying this expression (use keyword MEAN) |
|
| Delete rows with Median satisfying this expression (use keyword MEDIAN) |
|
| Delete Rows with number of missing values satisfying this expression (use keyword NMISS) |
|
| Delete rows with Percentile satisfying this expression (use keyword PCTL) |
|
| Delete rows with Standard Deviation satisfying this expression (use keyword STD) |
|
| Density Smoothing Bandwidth Computation Method |
|
| Density Smoothing Bandwidth Multiplier |
|
| Description |
|
| Design-Level By Variables |
|
| Design-Level Grouping Variables |
|
| Differential Expression Effects to Keep in the Normalized Data |
|
| Direction of the Cutoff |
|
| Display Cumulative Percentage of Summary plots |
|
| Display detailed distribution statistics and histograms |
|
| Display Format for Density Grid Points |
|
| Display side-by-side box plots |
|
| Display Scatterplot matrices |
|
| Display Standard Deviation versus Mean plots |
|
| Distribution |
|
| Model Distribution |
|
| DNA data is log-transformed |
|
| DNA Design Variables to be Added in Output Data Sets |
|
| DNA Intensity Input SAS Data Set |
|
| DNA Matching Variables |
|
| Effect Sizes |
|
| Experimental Design SAS Data Set |
|
| Experimental Design Data Set Corresponding to Baseline Reference Data Set |
|
| Experimental Design SAS Data Set of DNA Intensity |
|
| Experimental Design SAS Data Set of RNA Intensity |
|
| Experimental Factor Variables |
|
| Exponential Multiplier of Kernel Density |
|
| Extract Protocol |
|
| Feature Variable |
|
| Features Detected in Minimum Cells |
|
| Fifth Experimental Design Data Set |
|
| Fifth Tall Data Set |
|
| File Containing Estimate Statements |
|
| Filter data with Zero or Missing values |
|
| Filter Rows Whose Proportion of Zero/Missing Values Exceeds this Cutoff |
|
| Filter to Include Annotation Rows |
|
| Filter to Include Observations |
|
| Filter to Include Rows |
|
| Filter to Include Secondary Annotation Rows |
|
| Filtered Output Data Set Name |
|
| Filtration Method for Data Points with Large Residuals |
|
| First Experimental Design Data Set |
|
| First Tall Data Set |
|
| Fixed Effects for Differential Expression |
|
| Flagging Output Data Set Name |
|
| Folder of Raw Data Files |
|
| Folder of Track Settings Files |
|
| Format |
|
| Fourth Experimental Design Data Set |
|
| Fourth Tall Data Set |
|
| GenBank Accession Variable |
|
| Gene Description Variable |
|
| Gene ID Variable |
|
| Gene Length Data Set |
|
| Gene Length Variable |
|
| Gene Symbol Variable |
|
| Gradient Convergence Criterion [1,1000000] |
|
| Group Percentage for Deletion |
|
| Growth Protocol |
|
| Hyb Protocol |
|
| ID |
|
| ID Variable |
|
| In Mean plots, size Error Bars using: |
|
| Include adjusted p-values in addition to -log10 (p-values) |
|
| Include exponentiated Estimates and Differences |
|
| Include Fold Changes in Addition to Log Fold Changes |
|
| Include Fold Changes in Addition to Log2 Fold Changes |
|
| Include group statistics in Output Data Set |
|
| Include p-values in addition to -log10 (p-values) |
|
| Include simple Differences only |
|
| Include Standard Errors |
|
| Include t-Statistics |
|
| Input data is log-transformed |
|
| Input SAS Data Set |
|
| Input x and y Data Set |
|
| Input z Data Set |
|
| Intensity Columns to Filter |
|
| JMP Journal Output File |
|
| JMP Script Output File Name |
|
| JSL Output File |
|
| Keep 0 Values without normalizing |
|
| Kenward-Roger Degrees of Freedom Method |
|
| Key Variable(s) to Associate with Input SAS Data Set |
|
| Key Variable(s) to Merge with Input SAS Data Set |
|
| Key Variables for Merging |
|
| Label |
|
| Label Protocol |
|
| Label Variable |
|
| Lambda Number |
|
| Link Function |
|
| List all model fits |
|
| List every model fit |
|
| List-Style Specification of Intensity Columns to Filter |
|
| List-Style Specification of Variables |
|
| List-Style Specification of Variables for Which to Display Distributions |
|
| List-Style Specification of Variables to Be Standardized |
|
| List-Style Specification of With Variables |
|
| Loess Weight Data Set |
|
| -log10(p-Value) Cutoff |
|
| Log Transformation of Measurements |
|
| Log transformed Output Data Set |
|
| Manufacturer |
|
| Manufacturer protocol |
|
| Match case for key variables |
|
| Maximum Dispersion to Filter Genes |
|
| Maximum Filtering Loops |
|
| Maximum Mean to Filter Genes |
|
| Maximum Number of Principal Components to Apply |
|
| Maximum z Value |
|
| Merge Annotation into Residuals Data Set |
|
| Merge Key Variables |
|
| Merge Key Variables to Associate with Input SAS Data Set |
|
| Minimum Dispersion to Filter Genes |
|
| Minimum Distance Between Genotyping Groups |
|
| Minimum Mean to Filter Genes |
|
| Minimum Ratio Range Between 2 Homozygous Groups |
|
| Minimum z Value |
|
| Mixed Model Expression Index Output Data Set Name |
|
| Mixed Model Output Data Set Name |
|
| Mixed Model Output Data Set Prefix |
|
| MMEI Output Data Set Name |
|
| Molecule |
|
| Multiple Testing Fixed Effects |
|
| Multiple Testing Method |
|
| Multipliers of Design Size |
|
| New Batches from Previous Batches |
|
| Normalized Response Filter Expression |
|
| Number of By Groups to Process at a Time |
|
| Number of Clusters |
|
| Number of Density Grid Points |
|
| Number of Discrete Classes to Use in Plots |
|
| Number of Factors to Subtract from the Data |
|
| Number of the First Principal Component for VCA |
|
| Number of First Principal Component to Model |
|
| Number of Last Principal Component to Model |
|
| Number of LOESS Iterations |
|
| Number of PLS Components |
|
| Number of Principal Components |
|
| Number of Random Splits |
|
| Number of Rows to Process at a Time |
|
| Number of Standard Deviations in Error Bars |
|
| Number of Variable Genes to Keep |
|
| Number of x Blocks |
|
| Number of x Grid Points |
|
| Number of y Blocks |
|
| Number of y Grid Points |
|
| Numerical Parameter for Advanced Standardization Methods |
|
| Only compute overall F-Test for Fixed Effects for Differential Expression |
|
| Organism |
|
| Organism(s) |
|
| Origin Corner |
|
| Other Columns to Include |
|
| Output Batch Profile Data Set |
|
| Output Coordinates Data Set |
|
| Output Data Set |
|
| Output Data Set Containing Filtered Data |
|
| Output Data Set for Graphs |
|
| Output Data Set for MA Plot |
|
| Output Data Set Name |
|
| Output Data Set of KDMM Factors |
|
| Output Data Set of Rescaling Factors |
|
| Output Data Set of RPM Factors |
|
| Output Data Set of TMM Factors |
|
| Output Data Set of TPM Factors |
|
| Output Data Set of Upper Quartile Factors |
|
| Output Data Set Prefix |
|
| Output Eigenvalues Data Set |
|
| Output Experimental Design Data Set |
|
| Output File Prefix |
|
| Output File Primary Title |
|
| Output File Secondary Title |
|
| Output Folder |
|
| Output HTML File |
|
| Output Normalized Data Set |
|
| Output experimental samples only |
|
| Output Plotting Data Set |
|
| Output Ratio Data Set |
|
| Output Statistics Data Set |
|
| Output Surface Data Set |
|
| Output Tall Data Set |
|
| Output Test Data Set |
|
| Output Updated Batch Profile Data Set |
|
| Output Variance Components Data Set |
|
| Overall Design |
|
| Overlay density estimates |
|
| PCA Plot Grouping Variables |
|
| PDF or RTF Output File |
|
| PDF or RTF Output File Name |
|
| Percentage of Data to Be Included in Training Data |
|
| Percentage of Nonmissing and Nonzero Data to Be in Training Subset |
|
| Percentile to Compute for PCTL Statistic |
|
| Percentage of Data on A Component to Be Trimmed |
|
| Percentage of Data on M Component to Be Trimmed |
|
| Percentage of Data to Be Trimmed before Summary [0,50] |
|
| Percentage of Mitochondria Genes Allowed |
|
| Percentile to Impute |
|
| Perform log2 transform after standardization |
|
| Perform within-array Loess normalization |
|
| Platform |
|
| Platform Contributors |
|
| Platform Data Set |
|
| Platform Organism |
|
| Platform Title |
|
| Plot Rate |
|
| Plot standardized residuals |
|
| Plot Variable 1 Axis Label |
|
| Plot Variable 2 Axis Label |
|
| Plotting Variables |
|
| Position Variable |
|
| Prefix for Experimental Design Output Data Set Names |
|
| Prefix for Tall Output Data Set Names |
|
| Primary Title to use in Plots |
|
| PROC FACTOR Options |
|
| PROC GLIMMIX Options |
|
| PROC MIXED Options |
|
| PROC MIXED Statements |
|
| PROC MIXED/GLIMMIX Statements |
|
| PROC PLS Options |
|
| Pseudo-Likelihood Convergence Criterion |
|
| PubMed ID |
|
| QC Data Set |
|
| Random Effects |
|
| Random Number Seed |
|
| Random Number Seed for Picking Random Subset |
|
| Randomly split the data |
|
| Ratio Output Data Set |
|
| Raw Data File(s) |
|
| Reference Variable |
|
| Reference Variable to Be Applied as the Baseline |
|
| Remove duplicate columns |
|
| Repeats |
|
| Replace intensities falling at least this many Standard Deviations above the Column Mean |
|
| Replace intensities falling at least this many Standard Deviations below the Column Mean |
|
| Replace intensities falling above this column percentile |
|
| Replace intensities falling above this value |
|
| Replace intensities falling below this Column Percentile |
|
| Replace intensities falling below this value |
|
| Replace highest values |
|
| Replace lowest values |
|
| Rescale the data based on the total measurements in the Training data set |
|
| Residual Cutoff |
|
| Residual False Positive Rate |
|
| Response Filter Expression |
|
| Response Variable Axis Label |
|
| Result Data Set |
|
| RNA data is log-transformed |
|
| RNA Design Variables to be Added in Output Data Sets |
|
| RNA Intensity Input SAS Data Set |
|
| RNA Matching Variables |
|
| RNA Output Data Set |
|
| Round normalized count data to integer |
|
| Row Index Variable |
|
| Row-Level Categorical Variables |
|
| Sample Description |
|
| Sample Name |
|
| Scale rows |
|
| Scaling Approach |
|
| Scan Protocol |
|
| Second Experimental Design Data Set |
|
| Second Tall Data Set |
|
| Secondary Annotation Chromosome Variable |
|
| Secondary Annotation Label Variable |
|
| Secondary Annotation Merge Variables |
|
| Secondary Annotation Position Variable |
|
| Secondary Annotation SAS Data Set |
|
| Select Comparison Set for Differential Expression Tests |
|
| Select Comparison Set for Mean Differences Tests |
|
| Select Training subset based on Missing status |
|
| Separate and journal results by chromosome |
|
| Separate results based on Design-Level By Variables |
|
| Series Title |
|
| Series Variables |
|
| Server Output Directory |
|
| Set flagging data to Missing |
|
| Set negative values to Missing before imputing |
|
| Shifting Factor |
|
| Shrink variances using Empirical Bayes |
|
| Smoothing Bandwidth Multiplier |
|
| Smoothing Parameter |
|
| SNP ID Variable |
|
| Sort VCA Plots by Weighted Average Proportion of Variation |
|
| Source Name |
|
| Split by these variables |
|
| Standardization Method |
|
| Standardization Method for Comparing Means |
|
| Standardization Method for Difference Tests |
|
| Standardization Statistics Input SAS Data Set |
|
| Standardize |
|
| Standardize Batch profile |
|
| Standardize KDMM factor |
|
| Standardize TMM Scaling Factor |
|
| Standardized Residuals Output Data Set Name |
|
| Statistic to Impute |
|
| Study |
|
| Sub-Feature Variable |
|
| Subject Variable |
|
| Subset Data Set to Use for Normalization |
|
| Summary |
|
| Summary Statistic |
|
| Support |
|
| Technology |
|
| Third Experimental Design Data Set |
|
| Third Tall Data Set |
|
| Threshold |
|
| Time to Event Variable |
|
| Title |
|
| Track Settings Files |
|
| Transposed Output Data Set |
|
| Treatment Protocol |
|
| Type of Correlation |
|
| Model Data As: |
|
| Unbounded Variance Component Estimates |
|
| Uniformly scale histograms in Detail plots |
|
| Uniformly scale y-axes in Volcano and Chromosome Position plots |
|
| Uniformly scale y-axes in Volcano plots |
|
| Use pooled Estimate of Variance |
|
| Value Definition |
|
| Value of Columns above to Be Associated with Control |
|
| Value of Columns above to Be Associated with Non-autosomes |
|
| Value of the Censor Variable that Indicates Censoring |
|
| Value of Variable Above to Be Used as Denominator |
|
| Value to Use to Replace Highest Values |
|
| Value to Use to Replace Lowest Values |
|
| Value of Columns above to Be Associated with Reference |
|
| Values of ID Variable to Plot |
|
| Variable Containing Names of Loess Weight Data Set Columns |
|
| Variable Defining the Ratio |
|
| Variable Gene Selection Method |
|
| Variables |
|
| Variables by Which to Merge Annotation Data |
|
| Variables by Which to Merge Annotation Data 1 |
|
| Variables by Which to Merge Annotation Data 2 |
|
| Variables By Which to Merge Filter Data Set |
|
| Variables by Which to Merge Primary Annotation Data |
|
| Variables by Which to Merge Secondary Annotation Data |
|
| Variables Defining Analysis Groups |
|
| Variables Defining Blocks |
|
| Variables Defining Control Sets |
|
| Variables Defining Groups |
|
| Variables Defining Groups for Mean Processing |
|
| Variables for Which to Display Distributions |
|
| Variables to Keep in Output |
|
| Variables to Be Normalized |
|
| Variables to Be Standardized |
|
| Variance Component Effects |
|
| Variables to Include in the Imputation Process |
|
| Weblink |
|
| Weighted With Kernel Density |
|
| Where Clause for Subsetting Input Data Set in Test Run |
|
| Winsor Rate |
|
| With Variables |
|
| Within Sub-Feature Median |
|
| Mean Difference Filter Cutoff |
|
| x-Coordinate Variable |
|
| y-Coordinate Variable |
|
| z-Coordinate Variables |
|
| Additional PROC CLUSTER Options |
|
| Additional PROC DISTANCE Options |
|
| Additional PROC TREE Options |
|
| Alpha |
|
| Annotation Chromosome Variable |
|
| Annotation Column Name Variable |
|
| Annotation Group Variable |
|
| Annotation Label Variable |
|
| Annotation Merge Variables |
|
| Annotation Position Variable |
|
| Annotation SAS Data Set |
|
| Annotation Variables to Keep |
|
| By Variables |
|
| Categorical Variables |
|
| Center Columns |
|
| Center Rows |
|
| Clustering Method |
|
| Color row profiles by: |
|
| Color Theme for Heat Map |
|
| Color Variable |
|
| Compare Variables |
|
| Compute Covariances Instead of Correlations |
|
| Compute Pearson covariances instead of correlations |
|
| Compute results for annotated rows only |
|
| Continuous Variables |
|
| Correlation Radius for Clustering |
|
| Covariates for Partial Correlations |
|
| Cutoff Level of Tree Axis |
|
| Design Color Variables |
|
| Design Label Variable |
|
| Display clustered heat map |
|
| Distance Metric |
|
| Distance Variables |
|
| Double center multiplicatively |
|
| Experimental Design SAS Data Set |
|
| Filter to Include Annotation Rows |
|
| Filter to Include Observations |
|
| Filter to Include Observations from the Primary Data Set |
|
| Filter to Include Observations from the Secondary Data Set |
|
| Filter to Include Primary Variables |
|
| Filter to Include Secondary Variables |
|
| GenBank Accession Variable |
|
| Gene Description Variable |
|
| Gene ID Variable |
|
| Gene Symbol Variable |
|
| Group Percentage for Row Inclusion |
|
| Hierarchical Clustering Method |
|
| ID Variable |
|
| ID Variables |
|
| Impute missing values for clustering |
|
| Include 3D plots |
|
| Include rows if: |
|
| Include rows with Interquartile Range satisfying this expression |
|
| Include rows with Mean satisfying this expression |
|
| Include rows with Median satisfying this expression |
|
| Include rows with Percentile satisfying this expression |
|
| Include rows with Standard Deviation satisfying this expression |
|
| Increment Between Lower and Upper Values |
|
| Input SAS Data Set |
|
| Input Data Set is a Distance Matrix |
|
| Intensity Columns to Plot |
|
| JMP Script Output File Name |
|
| JSL Output File |
|
| K-Means Clustering Method |
|
| Label Variable |
|
| Level of Measurement |
|
| List every model fit |
|
| List-Style Specification of Categorical Variables |
|
| List-Style Specification of Continuous Variables |
|
| List-Style Specification of Covariates for Partial Correlations |
|
| List-Style Specification of Distance Variables |
|
| List-Style Specification of Intensity Columns to Plot |
|
| List-Style Specification of Primary Set of Variables |
|
| List-Style Specification of Secondary Set of Variables |
|
| List-Style Specification of Variables to Compute Distances/Clustering Across |
|
| List-Style Specification of Variables to Plot |
|
| List-Style Specification of Variables Whose Rows Are to Be Clustered |
|
| -log10(p-Value) Cutoff |
|
| -log10(p-Value) Cutoff for Output Test Data Set |
|
| Lower Number of Dimensions to Fit |
|
| Maximum Number of Clusters |
|
| Merge Key Variables |
|
| Multiple Testing Method for Output Test Data Set |
|
| Number of Clusters |
|
| Number of Primary Set of Variables to Process at a Time (log10 Scale) |
|
| Number of Principal Components |
|
| Number of Secondary Set of Variables to Process at a Time (log10 Scale) |
|
| Number of Variables to Process at a Time |
|
| Numerical Parameter for Advanced Standardization Methods |
|
| Options to Define Cluster Membership |
|
| Ordering Variable |
|
| Organism |
|
| Output Data Set |
|
| Output Data Set Name |
|
| Output Data Set Prefix |
|
| Output File Prefix |
|
| Output Folder |
|
| Output Means Data Set |
|
| Output Test Data Set |
|
| Percentile to Compute for PCTL Statistic |
|
| Perform SAS-based clustering on the Distance Matrix |
|
| Plot |
|
| Plot clusters |
|
| Prefix for Naming Output Variables |
|
| Primary Annotation SAS Data Set |
|
| Primary Input SAS Data Set |
|
| Primary Set of Variables |
|
| PROC CORR Statement Options |
|
| PROC FASTCLUS Options |
|
| PROC MDS Options |
|
| PROC PLS Options |
|
| Process Group Size for Primary Variables |
|
| Process Group Size for Secondary Variables |
|
| Replace cluster means with representative observations |
|
| Scale columns |
|
| Scale rows |
|
| Secondary Annotation Column Name Variable |
|
| Secondary Annotation SAS Data Set |
|
| Secondary Annotation Variables to Keep |
|
| Secondary Input SAS Data Set |
|
| Secondary Set of Variables |
|
| Server Output Directory |
|
| SNP ID Variable |
|
| Standardization Method |
|
| Standardize variables before clustering |
|
| Study |
|
| Two Way Clustering |
|
| Type of Correlation |
|
| Upper Number of Dimensions to Fit |
|
| Use lower boundary constraint of 0 for K matrix covariance parameter |
|
| Variable to Define Tree Axis |
|
| Variables By Which to Merge Annotation Data |
|
| Variables by Which to Merge Annotation Data |
|
| Variables Defining Groups |
|
| Variables to Compute Distances/Clustering Across |
|
| Variables to Keep in Output |
|
| Variables to Keep in Output Data Set |
|
| Variables to Plot |
|
| Variables to Retain in Output Data Set |
|
| Variables Whose Rows are to Be Clustered |
|
| Weight Variable |
|
| Absolute Mean Difference Cutoff for Continuous Predictors |
|
| Absolute Proportion Difference Cutoff for Class Predictors |
|
| Add reflected y variable to binary model |
|
| Algorithm |
|
| Annotation SAS Data Set |
|
| Apply adaptive weights |
|
| Asymmetric Loss Evaluation Proportion |
|
| Asymmetric Loss Fitting Proportion |
|
| Automated Model Type |
|
| Average Pool Size |
|
| Binary Dependent Variable Event Value |
|
| Binary Target Variable Event Value |
|
| Block Partition Variable |
|
| Boosted Fraction of Training Observations in a Single Tree |
|
| Boosted Maximum Number of Iterations |
|
| Boosted or Forest Random Number Seed |
|
| Boosted Shrinkage Factor |
|
| Categorical Covariates |
|
| Categorical Variables |
|
| Censor Variable |
|
| Centroid or Distance Summarization Method |
|
| Change output folder in Settings moved to right panel |
|
| Chromosome ID |
|
| Chromosome Label |
|
| Chromosome Number |
|
| Color Variable |
|
| Color Variables |
|
| Combined Output Data Set Name |
|
| Compute Individual Model Fits |
|
| Compute near optimal low-rank randomized SVD for the additive and dominance matrices |
|
| Continuous Covariates |
|
| Continuous Variables |
|
| Correlation Radius for Clustering |
|
| Criterion for Stopping Model Selection |
|
| Current Review |
|
| Custom Costs |
|
| Custom Prior Probabilities |
|
| CV Partitioning Method |
|
| Data Columns to be Transposed |
|
| Data Step Statements |
|
| Degrees of Freedom Hyper-parameter |
|
| Dependent Categorical Variable |
|
| Dependent Class Variable |
|
| Dependent Variable |
|
| Dependent Variables |
|
| Display Frobenius Measure |
|
| Distance Metric for Analysis |
|
| Distance Metric |
|
| Distribution |
|
| Early Stopping Threshold |
|
| Elastic Net L2 Penalty |
|
| Expected Proportion of Variance Explained by the Regression Model |
|
| Experimental Design Data Set |
|
| Experimental Design SAS Data Set |
|
| Feature Selection Criterion |
|
| Filter for BLUP Coefficients |
|
| Filter for PLS Coefficients |
|
| Filter to Include Markers |
|
| Filter to Include Observations |
|
| Filter to Include Predictor Categorical Variables |
|
| Filter to Include Predictor Continuous Variables |
|
| Fixed Effects |
|
| Fixed Test Data Set |
|
| Fixed Test Set |
|
| Folder of CVMC Results 1 |
|
| Folder of CVMC Results 2 |
|
| Folder of CVMC Results 3 |
|
| Folder of CVMC Results 4 |
|
| Folder of CVMC Results 5 |
|
| Folder of Predictive Modeling Settings |
|
| Folder of Settings Files |
|
| Folder of Test Data Sets |
|
| Folder of Test Sets |
|
| For Nominal Dependent Variables, compute distances to: |
|
| For Nominal Target Variables, compute distances to: |
|
| Forest Max Number of Variables to Compute Predictor Importance |
|
| Forest Max Number of Variables to Consider for Splitting a Node |
|
| Forest Maximum Number of Trees |
|
| Forest: Output filtered predictors list |
|
| Generate HTML Output |
|
| Group Variable |
|
| Grouping Variable |
|
| Groups Variable |
|
| Heterogeneous Variance Components |
|
| Hold-Out Method |
|
| Hold-Out Size, Specify as: |
|
| ID Variable |
|
| ID Variables |
|
| Impute zeros for missing continuous predictor values |
|
| Impute zeros for missing values |
|
| Include 3D plots |
|
| Include Dominance Effects |
|
| Increase R Software memory limit |
|
| Inner Loop Algorithm |
|
| Input SAS Data Set |
|
| Input Tall Data Set |
|
| Input Wide Data Set |
|
| Iteration End Number |
|
| Iteration Start Number |
|
| JMP Script Output File Name |
|
| K for K-Fold CV |
|
| K for K-Fold or 1/K Hold-Out |
|
| Kernel Function |
|
| Kernel Function for Computing Posterior Probabilities |
|
| L for Leave-L-Out |
|
| L1 Regularization Parameter |
|
| L2 Regularization Parameter |
|
| Label Variable |
|
| Link Function |
|
| List every model fit |
|
| List SAS Output for all model fits |
|
| List-Style Specification of Continuous Variables |
|
| List-Style Specification of Data Columns to be Transposed |
|
| List-Style Specification of Lock-In Categorical Predictor Variables |
|
| List-Style Specification of Lock-In Class Predictor Variables |
|
| List-Style Specification of Lock-In Continuous Predictor Variables |
|
| List-Style Specification of Lock-In Marker Variables |
|
| List-Style Specification of Marker Variables |
|
| List-Style Specification of Pedigree Relationship Matrix Variables |
|
| List-Style Specification of Predictor Categorical Variables |
|
| List-Style Specification of Predictor Continuous Variables |
|
| List-Style Specification of Variables to Be Standardized |
|
| Lock-In Categorical Predictor Variables |
|
| Lock-In Class Predictor Variables |
|
| Lock-In Continuous Predictor Variables |
|
| Lock-In Marker Variables |
|
| -log10(p-Value) Cutoff |
|
| log10 Regularization Parameter |
|
| Lower Bound for Target Variable |
|
| Marker Label |
|
| Marker Physical Position |
|
| Marker Position |
|
| Marker Variables |
|
| Max Number of Categories Allowed in a Predictor |
|
| Max Number of Effects in the Model |
|
| Max Number of Variables to Consider for Splitting a Node |
|
| Maximum Depth of Tree |
|
| Maximum Number of Buckley-James Iterations |
|
| Maximum Number of Filtered Predictors |
|
| Maximum Number of Grid Nodes to Use |
|
| Maximum Number of K-Means Clusters / Predictors |
|
| Maximum Number of Predictors to Use |
|
| Maximum Number of Steps |
|
| Maximum Number of Trees |
|
| Maximum Number of Variables to Select with Model Averaging |
|
| Maximum Number of Variables to Select with Pooling |
|
| Maximum Order of Interactions |
|
| Maximum Size of Training Set |
|
| Maximum Time for Area under Survival Curves |
|
| Method |
|
| Metric |
|
| Minimum Number of Observations Required for a Branch |
|
| Minimum Number of Observations Required for a Categorical Value |
|
| Minimum Size of Training Set |
|
| Minimum Time for Area under Survival Curves |
|
| Mode |
|
| Model Selection Method |
|
| Multiple Testing Method |
|
| Nominalize Continuous Dependent Variables |
|
| Number of Burn In Samples |
|
| Number of Generations |
|
| Number of Grid Points for Each Learning Curve |
|
| Number of Iterations |
|
| Number of model averaging samples |
|
| Number of Nearest Neighbors |
|
| Number of PLS Components |
|
| Number of power iterations (q) for the randomized SVD |
|
| Number of Predictor Variables to Select |
|
| Number of Predictors Included in Model |
|
| Number of Principal Components |
|
| Number of Random Hold-Out Iterations |
|
| Number of Random Iterations |
|
| Number of Rounds of Selection |
|
| Number of Rows in Input Data to Use in Test Run |
|
| Number of BLUPs to Use in Prediction |
|
| Number of Subsets Containing a Particular Variable |
|
| Numerical Parameter for Advanced Standardization Methods |
|
| Optimize the continuous predictor set |
|
| Outer Loop Test Set |
|
| Output Data Set |
|
| Output Data Set Name |
|
| Output Data Set Prefix |
|
| Output Experimental Design Data Set |
|
| Output Folder |
|
| Output Tall Data Set |
|
| Output Wide Data Set |
|
| P for P-Percent-Hold-Out |
|
| Pedigree Relationship Matrix Variables |
|
| Perform Buckley-James Estimation |
|
| Perform Cross Validation Model Comparison |
|
| Perform Learning Curve Model Comparison |
|
| Perform model averaging |
|
| Perform poolwise selection |
|
| Perform recoding with respect to: |
|
| Plot Separate Charts |
|
| Plot weights for predictor variables |
|
| Predictor Categorical Variables |
|
| Predictor Continuous Variables |
|
| Prefix for Tall Column Names |
|
| Prefix for Wide Column Names |
|
| Primary Input SAS Data Set |
|
| Primary Output Data Set Name |
|
| Prior Probabilities / Prevalences |
|
| PROC DISCRIM Options |
|
| PROC DISTANCE Options |
|
| PROC GENESELECT Statement Options |
|
| PROC GLIMMIX Additional Statements |
|
| PROC GLIMMIX Class Variables |
|
| PROC GLIMMIX Fixed Effects |
|
| PROC GLIMMIX MODEL Statement Options |
|
| PROC GLIMMIX Statement Options |
|
| PROC GLMSELECT Modeling Options |
|
| PROC GLMSELECT Statement Options |
|
| PROC HPMIXED Additional Statements |
|
| PROC HPMIXED Class Variables |
|
| PROC HPMIXED Fixed Effects |
|
| PROC HPMIXED MODEL Statement Options |
|
| PROC HPMIXED Statement Options |
|
| PROC LIFEREG Modeling Options |
|
| PROC LIFEREG Statement Options |
|
| PROC LOGISTIC MODELING Options |
|
| PROC LOGISTIC Response Options |
|
| PROC LOGISTIC Statement Options |
|
| PROC MIXED Additional Statements |
|
| PROC MIXED Class Variables |
|
| PROC MIXED Fixed Effects |
|
| PROC MIXED MODEL Statement Options |
|
| PROC MIXED Statement Options |
|
| PROC PHREG Modeling Options |
|
| PROC PHREG Statement Options |
|
| PROC PLS Statement Options |
|
| PROC QUANTSELECT Statement Options |
|
| PROC QUANTSELECT Modeling Options |
|
| Quantile Level |
|
| Quantile Level for Quantile Regression |
|
| R Software Memory Size (Mb) |
|
| Random Number Seed |
|
| Random Number Seed for Forest |
|
| Random Number Seed for Randomize SVD |
|
| Reference Time for Comparing Survival Curves |
|
| Reference Times for Comparing Survival Curves |
|
| Regard missing values as valid for prediction |
|
| Regression Model |
|
| Root Mean Square Error Convergence Tolerance |
|
| Rule Mix Maximum Number of Initial Rules |
|
| Rule Mix Maximum Number of Secondary Rules |
|
| SAS Procedure |
|
| Scale Hyper-parameter |
|
| Secondary Input SAS Data Set |
|
| Secondary Output Data Set Name |
|
| Separate Bar Charts for Each Model |
|
| Separate Bar Charts for Each Test Set |
|
| Separate Charts for Each Model |
|
| Separate Charts for Each Test Set |
|
| Server Output Directory |
|
| Settings Files |
|
| Settings for Which to Construct Learning Curves |
|
| Settings to Cross Validate |
|
| Settings to Use for Test Data Set Evaluation |
|
| Settings to Use for Test Set Evaluation |
|
| Significance Level for Adding Variables |
|
| Significance Level for Keeping Variables |
|
| Significance Level for Retaining Variables |
|
| Similarity Measure |
|
| SL for Adding Variables |
|
| SL for Keeping Variables |
|
| SL for Retaining Variables |
|
| Standardization Method for Predictor Continuous Variables |
|
| Standardize Predictors Row-Wise |
|
| Statistical Testing Method for Continuous Predictors |
|
| Study |
|
| Target Categorical Variable |
|
| Target rank (k) of the low-rank randomized SVD |
|
| Target Variable |
|
| Target Variables |
|
| Test Data Set |
|
| Test Data Sets |
|
| Test Sets |
|
| Thinning Rate |
|
| Time to Event Variable |
|
| Transformation for Predictor Continuous Variables |
|
| Type of Dependent Variable |
|
| Type of Target Variable |
|
| Upper Bound for Target Variable |
|
| Usage of K-Means Clusters |
|
| Use Forest to create interaction indicators |
|
| Use Forest to filter predictors |
|
| Use Grid Computing |
|
| Use life regression to filter predictors |
|
| Use K-Means clustering to reduce predictors |
|
| Use Leave-One-Out error rate as the Fitness function |
|
| Use PROC HPLOGISTIC |
|
| Use simple Cox Proportional Hazards function to filter predictors |
|
| Use statistical testing to filter predictors |
|
| Validation Data Set |
|
| Value of the Censor Variable that Indicates Censoring |
|
| Values of the Censor Variable that Indicate Censoring |
|
| Variable Selection Method |
|
| Variables Defining Tall Column Names |
|
| Variables Defining Wide Column Names |
|
| Variables to Be Standardized |
|
| Weight for Censored Observations |
|
| Weight Variable |
|
| Weighting Function |
|
| Where Clause for Subsetting Input Data in Test Run |
|
| Alpha |
|
| Apply adaptive weights |
|
| Categorical Clustering Variables |
|
| Class Clustering Variables |
|
| Cluster Effect Type |
|
| Continuous Clustering Variables |
|
| Criterion for Stopping Model Selection |
|
| CV Partitioning Method |
|
| Dependent Variable |
|
| Direction of Enhanced Treatment Effect |
|
| Fixed Main Effects |
|
| Input SAS Data Set |
|
| JMP Script Output File Name |
|
| K for K-Fold CV |
|
| List-Style Specification of Categorical Clustering Variables |
|
| List-Style Specification of Class Clustering Variables |
|
| List-Style Specification of Continuous Clustering Variables |
|
| List-Style Specification of Predictor Categorical Variables |
|
| List-Style Specification of Predictor Continuous Variables |
|
| Main Effects Selection Method |
|
| Max Number of Variables to Consider for Splitting a Node |
|
| Maximum Depth of Tree |
|
| Maximum Number of Steps |
|
| Maximum Number of Trees |
|
| Maximum Order of Interactions |
|
| Minimum Number of Observations Required for a Branch |
|
| Minimum Number of Observations Required for a Categorical Value |
|
| Model Selection Method |
|
| Number of Bins for Continuous Variables |
|
| Number of Principal Components to Use for Propensity Scoring |
|
| Number of Resamples to Use for Computing Significance |
|
| Output Data Set Prefix |
|
| Output Folder |
|
| Predictor Categorical Variables |
|
| Predictor Continuous Variables |
|
| Random Number Seed |
|
| Random Number Seed for Forest |
|
| Regard missing values as valid for prediction |
|
| Relaxation Factor for Alpha |
|
| SL for Adding Variables |
|
| SL for Keeping Variables |
|
| Study |
|
| Target Variable |
|
| Treatment Control Level |
|
| Treatment Variable |
|
| Type of Dependent Variables |
|
| Use Interactions between treatment and predictor variables |
|
| Variable Selection Method |
|
| Variability Assumption |
|
| Weight Variable |
|
| Adjust all p-value variables together |
|
| Alpha |
|
| Annotation SAS Data Set |
|
| Annotation Merge Variables |
|
| Category Variable |
|
| Censor Limit (-log10 scale) |
|
| Censor Limit (-log or -log10 scale) |
|
| Create significance indicator columns |
|
| Effect Estimate or Direction Variable |
|
| Effect Estimate or Direction Variable is the odds ratio |
|
| Effect ID Variable |
|
| Filter to Include Annotation Rows |
|
| Filter to Include Observations |
|
| Folder of Input SAS Data Sets |
|
| ID Variable |
|
| Input SAS Data Set |
|
| Method to Use |
|
| Multiple Testing Method |
|
| Open Output Data Set |
|
| Other Effect Variables |
|
| Other ID Variables |
|
| Other p-Value Variables |
|
| Other Sample Size Variables |
|
| Other Standard Error Variables |
|
| Output Data Set |
|
| Output File Prefix |
|
| Output Folder |
|
| Output rows with a significant p-value only |
|
| p-Value Combination Method |
|
| p-Value Variable |
|
| p-Value Variables |
|
| Primary Delimiter Separating Annotation Categories |
|
| Sample Size Variable |
|
| SAS Data Sets |
|
| Secondary Delimiter |
|
| Server Output Directory |
|
| Standard Error Variable |
|
| Study |
|
| Study ID Variable |
|
| Tau Value for TPM |
|
| Transformation of Input p-Values |
|
| Transformation of Output Adjusted p-Values |
|
| Transformation of Output p-Values |
|
| Variables By Which to Merge Annotation Data |
|
| -log10(p-value) Cutoff |
|
| Additional Bandwidth on Each Side of Tracks |
|
| Alpha |
|
| Annotation Merge Variables |
|
| Annotation SAS Data Set |
|
| Annotation Variables to Keep |
|
| Bin Method |
|
| Bin Summary Statistic |
|
| Chromosome |
|
| Chromosome Color Theme Settings File |
|
| Chromosome Text Data Set |
|
| Chromosome Text File |
|
| Chromosome Variable |
|
| Chromosome Variable 1 |
|
| Chromosome Variable 2 |
|
| Coding Region End |
|
| Coding Region Start |
|
| Color of Bars ({r,g,b}) |
|
| Color Theme |
|
| Color Variable |
|
| Color Variable Type |
|
| Construct Color Theme using: |
|
| Continuous Variables to Plot |
|
| Create separate plots for each variable |
|
| Custom Track Variable |
|
| Description |
|
| Direction of Other Variables |
|
| Display output as a: |
|
| Circular Display |
|
| Draw indicator line |
|
| End |
|
| Exon Count |
|
| Exon Ends |
|
| Exon Starts |
|
| Filter to Include Annotation Rows |
|
| Filter to Include Observations |
|
| Folder of Chromosome Color Theme Settings Files |
|
| Folder of Track Settings Files |
|
| GenBank Accession Variable |
|
| Gene Description Variable |
|
| Gene Name or Identifier |
|
| Gene ID Variable |
|
| Gene Symbol Variable |
|
| Genome |
|
| Initial Color Theme |
|
| Initial Cutoff for Displaying Bars |
|
| Input GFF File |
|
| Input SAS Data Set |
|
| Label for Other Variables |
|
| Label |
|
| Label Variable |
|
| Lightness Scale |
|
| Links Color Theme |
|
| Links Color Variable |
|
| Links Input SAS Data Set |
|
| Multiple Testing Method |
|
| Name |
|
| Number of Legend Decimals |
|
| Number of Legend Levels |
|
| Number of Rows in Each Bin |
|
| Organism |
|
| Output Data Set |
|
| Output Folder |
|
| Plot bars |
|
| Plot markers with significant p-values only |
|
| Position |
|
| Position Variable |
|
| Position Variable 1 Start |
|
| Position Variable 1 Stop |
|
| Position Variable 2 Start |
|
| Position Variable 2 Stop |
|
| Primary Color |
|
| Reverse Color Theme |
|
| Saturation Scale |
|
| Search Type |
|
| Secondary Color |
|
| Server Output Directory |
|
| Set window size |
|
| SNP ID Variable |
|
| Start |
|
| Strand |
|
| Study |
|
| Summary Statistic Across Continuous Variables |
|
| Text Data Set |
|
| Text File |
|
| Threshold Indicator |
|
| Title of Custom Track |
|
| Track Settings Files |
|
| Transformation of Input p-Values |
|
| Transformation of Output p-Values |
|
| Transparency |
|
| Two Column Threshold |
|
| Type of Continuous Variables to Plot |
|
| Value at Which to Censor High Values |
|
| Value at Which to Censor Low Values |
|
| Value Ordering for Nominal Variables |
|
| Values at Which to Draw Horizontal Reference Lines |
|
| Variables By Which to Merge Annotation Data |
|
| Variables to Keep in HTML Data Set |
|
| Variables to Retain in HTML Data Set |
|
| Width of Bars |
|
| Width of Positional Bin |
|
| Window Size |
|
| y Variable |
|
| y Variables |
|
| -log10(p-Value) Cutoff |
|
| Affymetrix Array Type |
|
| Affymetrix GeneChip Array |
|
| Affymetrix Link |
|
| Agilent Array Type |
|
| Alpha |
|
| AmiGO Database Link |
|
| Annotation Merge Variables |
|
| Annotation SAS Data Set |
|
| Annotation Variables to Keep |
|
| Applied BioSystems Array Type |
|
| Categorical Phenotype Variable |
|
| Category Variable |
|
| Category Variables |
|
| Check uniqueness of column names |
|
| Chromosomal Location |
|
| Chromosome |
|
| Codelink Array Type |
|
| Compress output data sets |
|
| Continuous Phenotype Variables |
|
| Control Levels |
|
| Custom Track Variable |
|
| Data Step Statements |
|
| dbSNP ID |
|
| dbSNP Link |
|
| Description |
|
| Direction of Significance Variables |
|
| EC Database Link |
|
| End |
|
| Enrichment Tests |
|
| Ensembl Database Link |
|
| Ensembl ID |
|
| Entrez Gene ID |
|
| Entrez Databases Link |
|
| Entrez Gene Link |
|
| Entry Delimiter |
|
| Entry Id Delimiter |
|
| Enzyme ID (EC number) |
|
| Experimental Design SAS Data Set |
|
| Files to Import |
|
| Filter to Include Annotation Rows |
|
| Filter to Include Observations |
|
| Folder of List Files |
|
| Folder of Raw Files |
|
| GenBank Accession |
|
| GenBank Link |
|
| Gene Description |
|
| Gene Description Variable |
|
| Gene ID |
|
| Gene Identifier Variable |
|
| Gene Name or Identifier |
|
| Gene Name Variable |
|
| Gene/Protein Identifier |
|
| Gene Set Summary Method |
|
| Gene Symbol |
|
| Genome |
|
| GO ID |
|
| HGNC (Gene Symbol) Database Link |
|
| High Color RGB |
|
| High Hit Total Threshold |
|
| Homologene |
|
| ID Variable |
|
| Illumina Array Type |
|
| Ingenuity Canonical Pathway Membership Data (CSV file) |
|
| Ingenuity knowledge Base |
|
| Ingenuity Server |
|
| Input GMT File of Gene Sets |
|
| Input SAS Data Set |
|
| IPA Entry Point |
|
| IPA Project Name |
|
| JSL Output File |
|
| List Description File |
|
| Low Color RGB |
|
| Low Hit Threshold |
|
| Map Viewer Database Link |
|
| Maximum Category Length |
|
| Maximum Column Length |
|
| Method for Computing Reference Level for Each Gene |
|
| Middle Color RGB |
|
| Multiple Testing Method for Adjusting p-Values |
|
| Number of Bins for Cochran-Armitage Tests |
|
| Number of Bootstrap or Permutation Samples |
|
| Number of Genes to Process at a Time |
|
| Number of Rows to Scan |
|
| OMIM Database Link |
|
| OMIM ID |
|
| Organism |
|
| Organism-specific code |
|
| Output Data Set |
|
| Output Data Set Containing Categories |
|
| Output Data Set Containing Category Indicators |
|
| Output Data Set Containing Statistics |
|
| Output Data Set Name |
|
| Output File Name |
|
| Output File Type |
|
| Output Folder |
|
| Parse associated gene column |
|
| Percentile to Use as the Highest Color Value |
|
| Percentile to Use as the Lowest Color Value |
|
| Platform |
|
| Prefix for Output Data Set Names |
|
| Primary Delimiter Separating Annotation Categories |
|
| Probe ID |
|
| Probe Set or Gene ID |
|
| PubMed Database Link |
|
| Random Number Seed |
|
| Rank Transform Continuous Significance Variables for PAGE Tests |
|
| Reference Sequence Database Link |
|
| RefSeq ID |
|
| Row Reference Summary Statistic |
|
| Secondary Delimiter |
|
| Server Output Directory |
|
| Set window size |
|
| Significance Cutoff |
|
| Significance Input SAS Data Set |
|
| Significance Variable |
|
| Significance Variable Cutoff for Fisher Exact Tests |
|
| Significance Variables |
|
| Specify up to 20 IPA observations to upload |
|
| Standardize Rows based on Reference Group Standard Deviation |
|
| Start |
|
| Study |
|
| Swiss-Prot Database Link |
|
| Swiss-Prot ID |
|
| Title of Custom Track |
|
| Title of Custom Track |
|
| Type |
|
| Type of Gene Identifier |
|
| UniGene ID |
|
| UniGene Link |
|
| Use a proxy server to access the Web |
|
| Variables by Which to Color Pathways |
|
| Variables By Which to Merge Annotation Data |
|
| Variable Containing IDs |
|
| Variables Defining Analysis Groups |
|
| Variables Defining Control Sets |
|
| Variables to Keep in Gene-Level Output |
|
| Variables to Keep in Output |
|
| Variables to Retain in HTML Data Set |
|
| Window Size |
|
| 0-1 Variables |
|
| Access Documentation from the: |
|
| Add Filter Columns |
|
| Additional Fixed Effects |
|
| Additional PROC MIXED Statements |
|
| Additional SAS Data Step Statements |
|
| Affymetrix Array Type |
|
| Agilent Array Type |
|
| Alpha Values |
|
| Append Input Data Set |
|
| Append Input SAS Data Set |
|
| Applied BioSystems Array Type |
|
| Apply Original Column Names |
|
| Archive the resolved SAS macro code |
|
| Archive the SAS code |
|
| Array Variable |
|
| Auto clear |
|
| Base Input Data Set |
|
| Base Input SAS Data Set |
|
| Base SAS Data Set |
|
| By Variables |
|
| Categorical Variables |
|
| Channel Variable |
|
| Check uniqueness of column names |
|
| Codelink Array Type |
|
| Column Name Variable |
|
| Column Order Data Set |
|
| Column Variables |
|
| Compare Parameters Data Set |
|
| Compress output data set |
|
| Compress output data sets |
|
| Concatenate SAS Data Sets |
|
| Constant to Apply |
|
| Constants for Each Variance Component |
|
| Control Levels for Differential Expression Comparisons |
|
| Corresponding Key Variables from Merge Input Data Set |
|
| Corresponding Key Variables from Merge Input SAS Data Set |
|
| Data Columns to be Transposed |
|
| Data Set of Differences to Include from Comparison Set |
|
| Data Start Row |
|
| Data Step Statements |
|
| Default Annotation Folder |
|
| Default Input Folder |
|
| Default Library Folder |
|
| Default Narrative Template Folder |
|
| Default Output Folder |
|
| Default Server Output Directory |
|
| Default Settings Folder |
|
| Default Template Name |
|
| Delete nonmatching rows |
|
| Delete rows not in Base Input Data Set |
|
| Delete rows not in Base Input SAS Data Set |
|
| Delete rows satisfying this expression |
|
| Delete rows with at least this percentage of Missing values |
|
| Display Pre-Study Variable Requirements in terms of: |
|
| Drop numeric variables used to compute statistics |
|
| Drop Variables |
|
| Effect Sizes |
|
| Experimental Design Data Set |
|
| Experimental Design SAS Data Set |
|
| File Containing Estimate Statements |
|
| File Filter Expression |
|
| File Type |
|
| Files to Import |
|
| Filter to Include Observations |
|
| Filter to Include Observations (1) |
|
| Filter to Include Observations (2) |
|
| Filter to Include Observations (3) |
|
| Filter to Include Observations (4) |
|
| Filter to Include Tall Rows (and the corresponding Wide Variables) |
|
| Filter to Keep Observations |
|
| First Folder of Data Sets to Compare |
|
| Fixed Effects for Differential Expression |
|
| Folder Containing SAS Data Sets |
|
| Folder for UTF-8 Files after Converting |
|
| Folder of Non-UTF-8 Files |
|
| Folder of Raw Files |
|
| Force Append |
|
| Format |
|
| Frequency Variable |
|
| Gene/Protein Identifier |
|
| Hide reports with unsatisfied study requirements from Starter |
|
| Hide unchosen dialog options from requirements report |
|
| Hide unsatisfying studies from report dialogs |
|
| ID Variables |
|
| Illumina Array Type |
|
| Include |
|
| Include observations that meet: |
|
| Ingenuity Knowledge Base |
|
| Ingenuity Server |
|
| Input Data Set |
|
| Input Data Step Statements |
|
| Input SAS Data Set |
|
| Input Tall Data Set |
|
| Input Wide Data Set |
|
| IPA Entry Point |
|
| IPA Project Name |
|
| JMP Script Output File Name |
|
| Keep labels |
|
| Key Variables from Base Input Data Set |
|
| Key Variables from Base Input SAS Data Set |
|
| List of Variable Names and Lengths |
|
| List of Variable Names and Types |
|
| List-Style Specification of Data Columns to Be Transposed |
|
| List-Style Specification of Numeric Variables |
|
| List-Style Specification of Transpose Variables |
|
| List-Style Specification of Variables to Be Standardized |
|
| List-Style Specification of Variables to Be Summarized |
|
| List-Style Specification of Variables to Be Transformed |
|
| List-Style Specification of Variables to Reorder |
|
| List-Style Specification of Wide Variables Corresponding to Tall Rows |
|
| Match case for key variables |
|
| Maximum Column Length |
|
| Maximum Length for All Other (Unselected) Variables |
|
| Merge Input Data Set |
|
| Merge Input SAS Data Set |
|
| Merge Key Variables |
|
| Merge Key Variables (Venn Diagram - Multiple Tables) |
|
| Merge Key Variables to Associate with Input SAS Data Set |
|
| Metadata Server Name |
|
| Method for Handling Ties |
|
| Minimize lengths of selected variables |
|
| Minimum Number of Columns to Scan |
|
| Multipliers of Design Size |
|
| Name |
|
| Name of Response Variable |
|
| Name of this Settings Profile |
|
| New Label Specifications |
|
| New Length for Selected Variables |
|
| New Variable Names |
|
| Number of Columns to Use in Subset |
|
| Number of Groups for Rank Method GROUPS |
|
| Number of Rows to Scan |
|
| Numeric Variables over Which to Compute Row Statistics |
|
| Numerical Parameter for Advanced Standardization Methods |
|
| Output Data Set |
|
| Output Data Set for Graphs |
|
| Output Data Set Name |
|
| Output Data Step Statements |
|
| Output Experimental Design Data Set |
|
| Output Experimental Design Data Set Name |
|
| Output File |
|
| Output File Name |
|
| Output Folder |
|
| Output Stack Data Set |
|
| Output Statistics Data Set |
|
| Output Tall Data Set |
|
| Output Wide Data Set |
|
| Password |
|
| Percentile to Compute for PCTL Statistic |
|
| Percentile to Impute |
|
| Perform log2 transform after standardization |
|
| Platform |
|
| Port Number |
|
| Prefix |
|
| Prefix for Column Names in Tall Data Set |
|
| Prefix for Output Data Set Names |
|
| Prefix for Tall Column Names |
|
| Prefix for Wide Column Names |
|
| Pre-SET Data Step Statements |
|
| Pre-SET Output Data Step Statements |
|
| Print Options |
|
| PROC MIXED Options |
|
| Prompt about closing all associated graphics and tables when closing tabbed reports |
|
| Proportional Areas |
|
| Proportional Surrounding Area (applies only for 1-way, 2-way, and 3-way diagrams) |
|
| Proxy Port Number |
|
| Proxy Server Name |
|
| Random Effects |
|
| Random Number Seed |
|
| Rank Method |
|
| Rank Order |
|
| Rank Variables |
|
| Remove labels from these variables |
|
| Remove rows with duplicate values of Sort Variables |
|
| Remove variables not found |
|
| Replace value of counts with proportion of total counts |
|
| Repository Name |
|
| Response Variable |
|
| Row Number of Variable Names |
|
| Row Variables |
|
| SAS Code for Transformation |
|
| SAS Data Set Folder |
|
| SAS Drug Development Server URL |
|
| SAS File Folder |
|
| Save and Restore Current Row States |
|
| Second Folder of Data Sets to Compare |
|
| Select |
|
| Select Columns |
|
| Select Comparison Set for Differential Expression Tests |
|
| Select Missing |
|
| Server Output Directory |
|
| Set negative values to Missing before imputing |
|
| Shared Grid Folder (UNC path recommended) |
|
| Shared Grid Folder - Client Version |
|
| Shared Grid Folder - Server Version |
|
| Shifting Factor |
|
| Show |
|
| Show Starter Customization buttons |
|
| Show Variable Requirements and Usage link on report dialogs |
|
| Sort |
|
| Sort Variables |
|
| Specify a name for the 0-1 column |
|
| Specify up to 20 IPA observations to upload |
|
| Standardization Method |
|
| Standardization Statistics Input SAS Data Set |
|
| Standardize |
|
| Starting Values for 3-Way Optimization |
|
| Statistic to Compute |
|
| Statistic to Impute |
|
| Statistics to Compute |
|
| Study |
|
| Subset Data Set to Use for Normalization |
|
| Summary Statistic to Compute for Each Variable |
|
| Tall SAS Data Set |
|
| Transform Expression |
|
| Transport File Folder |
|
| Transport File Name |
|
| Transpose Variables |
|
| Transposed Output Data Set |
|
| Type |
|
| Type of Transformation |
|
| Use a subset of columns |
|
| Use Only Selected Rows when Comparing Tables |
|
| User Name |
|
| Variable Containing Current Column Names |
|
| Variable Containing Names of Wide Variables |
|
| Variable Containing New Column Names |
|
| Variable to Identify Individual Probe Set |
|
| Variables By Which to Summarize |
|
| Variables Defining Groups |
|
| Variables Defining Tall Column Names |
|
| Variables Defining Wide Column Names |
|
| Variables to Be Standardized |
|
| Variables to Be Summarized |
|
| Variables to Be Transformed |
|
| Variables to Drop |
|
| Variables to Drop from Output SAS Data Set |
|
| Variables to Exclude from the Output Stack Data Set |
|
| Variables to Include in the Imputation Process |
|
| Variables to Keep in Output Data Set |
|
| Variables to Keep in Output SAS Data Set |
|
| Variables to Reorder |
|
| Variables to Retain in Output Data Set |
|
| Variables Whose Length is to be Changed |
|
| Version of SDD instance: |
|
| Weight Variable |
|
| Wide SAS Data Set |
|
| Wide Variables Corresponding to Tall Rows |
|
| Using JMP Graphics in Presentations and Publications |
|
| Specifying Folders, Files, and Data Sets |
|
| Examining Folders, Files, and Data Sets |
|
| List-Style Specification |
|
| The SAS WHERE Expression |
|
| Estimate Statements and the Estimate Builder |
|
| Rules for Study Names |
|
| Rules for Paths |
|
| Rules for Review Package Names |
|
| JMP Genomics Files are Identified by Suffixes |
|
| JMP Genomics Processes Call SAS PROCS |
|
| Glossary |
|
| Trouble Shooting |
|
| References |
|
What do I need?
A JMP table containing at least one column of p-values of an arbitrary set of features (for example, genes, probesets, exons, markers) must be open and in focus before you can select and open the P-Value Quantile Plotter dialog.
For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.
Output/Results
Running this process adds a column (for each P-value variable specified) containing the transformed, observed p-values to the input data set and generates a plot (shown below) of the observed p-values versus the expected p-values for this data set.
The plot for the expected p-values is represented by the solid line running diagonally upward from the lower left. The observed -log10 p-values for these data are plotted with solid black dots. The observed p-values extending away from the reference line on the right hand side are the ones representing significant differences.