Output Description

One-Way ANOVA

Running this process using the XTitrationExample sample setting generates a JMP journal (shown below) containing links to the chromosome-specific analysis results as well as to the combined results. Refer to the One-Way ANOVA process description for more information.

Click Chromosome chr22 to open the tabbed Results window shown below. Output from the process is organized into tabs. Each tab contains one or more plots, data panels, data filters, and so on. that facilitate your analysis.

Note: Each of the tabbed Results windows for the analysis can be accessed from the Journal. All of these windows are similar to the one shown here.

The Results window contains the following panes:

Tabs

This pane enables you to access and view the output plots and associated data sets on each tab. Use the drop-down menu to view the tab in the Tab Viewer pane, open the tab in a new window, or remove the tab and its contents from the Tab Viewer pane.

The following tabs are generated by this process:

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Results: This tab shows the primary results from the analysis, including volcano plots and various analyses on least squares means.

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Ave Sig Index Chromosome Plots: This tab plots the proportion of the observed differences that are statistically significant by position on the specified chromosome.

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Variability Estimates: This tab shows the analyses on variance component estimates from the ANOVA model fits.

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Standardized Residual Plots: This tab shows the analyses on residual from the anova model fits when you have requested them in the dialog.

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Chromosome Position Plots: This tab shows a separate overlay plot for each chromosome of the meta-analysis p-value by chromosome location for the markers This tab is generated whenever a Chromosome Variable is specified.

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SAS Output: This is a text-based output directly from SAS PROC UNIVARIATE. Refer to the documentation for SAS PROC UNIVARIATE for more information.

Drill Downs

Action buttons provide you with an easy way to drill down into your data.

The following action buttons are generated by this process:

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IPA Upload: Select points or rows and click IPA Upload to open the IPA Upload process with the selected points specified as input data.

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UCSC Genome Browser: Select points or rows and click UCSC Genome Browser to open the UCSC Genome Browser process with the selected points specified as input data.

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Annotation Summary: Select points or rows and click Annotation Summary to summarize annotation information for the selected genes or markers

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GO Stat: Select points or rows and click GO Stat to access, annotate, and analyze information for selected molecular entities in the Gene Ontology database.

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Onto-Express: Select points or rows and click Onto-Express to retrieve annotation information for selected gene or markers from the Onto-Express database

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GenBank Nucleotide: Select points or rows and click GenBank Nucleotide to opens a browser window directed to a GenBank Nucleotide search for the selected molecular entities.

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UniGene Database: Select points or rows and click UniGene Database to open a browser window directed to a UniGene Database search for the selected molecular entities.

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AceView Database: Select points or rows and click View Data to access information from the ACEView database for selected genes or markers.

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Open Subset in Tall Format: Select points or rows and click Open Subset in Tall Format to create a tall version of the input data for the selected genes.

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Open Subset in Wide Format: Select points or rows and click Open Subset in Wide Format to create a wide version of the input data for the selected genes.

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Fit Model and Plot LS Means: Select points or rows and click Fit Model and Plot LS Means to select variable(s) that uniquely define wide column names. Selected genes are analyzed in the JMP Fit Model platform to view detailed fitting results and plots. Attention: Read the warning found in the link.

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Construct One-way Plots: Click Construct One-way Plots to plot the original data in one-way format using treatment variables of your choice.

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Launch Plot Intensities: Select points or rows and click Launch Plot Intensities to launch the Plot Intensities process on the selected genes.

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Venn Diagram: Click Venn Diagram to launch an open dialog from which you can select up to 5 comparisons and create a Venn diagram to display the overlap of significant genes from those comparisons.

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Launch JMP Genomics Browser: Select points or rows and click Launch JMP Genomics Browser to launch the JMP Genomics Browser process for the selected points.

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Create Subset with Mean Difference and P-value Criteria: Optionally select points in a graph. Click Create Subset with Mean Difference and P-value Criteria to create custom subsets based on mean differences and/or p-value cut offs that you specify in a window that appears after you click this action button. Each l probe with at least one of the results1 Specified using the Select One or More Mean Difference Columns field in the window that appears after you click this action button. satisfying all of the cutoff criteria specified (Mean Difference Filter Cutoff, Direction of the Cutoff, and -log10(p-value) Cutoff fields) is placed in the subset data set.

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Enter new -log10(p) cutoff: Enter a new value in the text box to change the horizontal dashed red line in the volcano plots that is used for determining statistical significance. Click Refresh to update all plots to reflect the new cutoff.

Output Data

This process generates the following data set:

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Significant Differences Data Set: This output data set contains a complete list of the genes significant by one or more criteria. This data set is indicated by the _sig suffix. Click Open to view the data set.

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Tab Viewer

This pane provides you with a space to view individual tabs within the Results window.

General

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Click View Data to reveal the underlying data table associated with the current tab.

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Click Reopen Dialog to reopen the completed process dialog used to generate this output.

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Click Create Report to generate a pdf- or rtf-formatted report containing the plots and charts of selected tabs.

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Click Close All to close all graphics windows and underlying data sets associated with the output.