ANOVA

Output | Expression | ANOVA

ANOVA

Running this process using the DrosophilaAgingExample sample setting generates the tabbed Results window shown below. Refer to the ANOVA process description for more information. 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.

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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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 residuals 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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Fixed Effects Tests :This tab shows the proportion of your data that can be explained by the specified fixed effects . This tab is generated whenever one or more Fixed Effects are specified.

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Goodness of Fit : This tab shows how well the count data fits with the specified model . It is generated for count data only.

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 AceView Database to access information from the ACEView database for selected genes or markers.

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PubMed : select points or rows and click PubMed to access information from the PubMed database for selected genes or markers.

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Entrez Cross : select points or rows and click Entrez Cross to access information from more than 25 NCBI databases.

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Entrez Gene : select points or rows and click Entre Gene to access information from NCBI's database for gene-specific information from genomes that have been completely sequenced or that are scheduled for intense sequence analysis.

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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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iPathwayGuide Output Data : Click iPathwayGuide Output Data to generate one or more txt files containing comparison levels that can be used for pathway analysis of your output data.

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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 probes with at least one of the results ¹ satisfying all of the cutoff criteria specified ( Mean Difference Filter Cutoff , Direction of the Cutoff , and -log 10 (p-value) Cutoff fields) is placed in the subset data set.

Note : This button is not surfaced unless LSMeans Effects are specified.

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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, including Fit Statistics. This data set is indicated by the _sig suffix. Click to view the data set.

Variables in this data set are named using the conventions in the table below:

SAS Variable Name

Description

Variance_Array

Variance of the array for each gene.

Variance_Residual

Variance of the residual for each gene.

Sum_Variance

Summary of the Varience_Array and Varience_Residual for each gene

PropVar_Array

Proportion of Array Variance. This is calculated by dividing the Variance_Array by the SumVariance .

RSquare

R Square: coefficient of determination

AIC

Akaike Information Criterion

AICC

Corrected Akaike Information Criterion

BIC

Bayesian information criterion

F_T3_ XX

F statistics for the type III test. F_T3 serves as a common prefix. The _XX suffix, appended to the prefix, indicates the specific variable(s) ( Sex or Age , for example) used in the analysis. When more than one variable is considered (the interaction of Sex by Age , for example) each variable is appended to the prefix as follows: F_T3_Sex_Age .

NDF_T3_ XX

Numerator degrees of freedom for the type III test. NDF_T3 serves as a common prefix. The _XX suffix, appended to the prefix, indicates the specific variable(s) ( Sex or Age , for example) used in the analysis. When more than one variable is considered (the interaction of Sex by Age , for example) each variable is appended to the prefix as follows: NDF_T3_Sex_Age .

DDF_T3_ XX

Denominator degrees of freedom for the type III test. DDF_T3 serves as a common prefix. The _XX suffix, appended to the prefix, indicates the specific variable(s) ( Sex or Age , for example) used in the analysis. When more than one variable is considered (the interaction of Sex by Age , for example) each variable is appended to the prefix as follows: DDF_T3_Sex_Age .

PrF_T3_ XX

Probability of the type III test = the p -value. PrF_T3 serves as a common prefix. The _XX suffix, appended to the prefix, indicates the specific variable(s) ( Sex or Age , for example) used in the analysis. When more than one variable is considered (the interaction of Sex by Age , for example) each variable is appended to the prefix as follows: PrF_T3_Sex_Age .

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

Launch Follow-up Processes

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Gene Set Enrichment : Click to launch the Gene Set Enrichment process with the Significant Differences Data Set preloaded as input.

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 surface the data sets corresponding to the active 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.

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Specified using the Select One or More Mean Difference Columns field in the window that appears after you click this action button.

SAS Variable Name	Description
Variance_Array	Variance of the array for each gene.
Variance_Residual	Variance of the residual for each gene.
Sum_Variance	Summary of the Varience_Array and Varience_Residual for each gene
PropVar_Array	Proportion of Array Variance. This is calculated by dividing the Variance_Array by the SumVariance .
RSquare	R Square: coefficient of determination
AIC	Akaike Information Criterion
AICC	Corrected Akaike Information Criterion
BIC	Bayesian information criterion
F_T3_ XX	F statistics for the type III test. F_T3 serves as a common prefix. The _XX suffix, appended to the prefix, indicates the specific variable(s) ( Sex or Age , for example) used in the analysis. When more than one variable is considered (the interaction of Sex by Age , for example) each variable is appended to the prefix as follows: F_T3_Sex_Age .
NDF_T3_ XX	Numerator degrees of freedom for the type III test. NDF_T3 serves as a common prefix. The _XX suffix, appended to the prefix, indicates the specific variable(s) ( Sex or Age , for example) used in the analysis. When more than one variable is considered (the interaction of Sex by Age , for example) each variable is appended to the prefix as follows: NDF_T3_Sex_Age .
DDF_T3_ XX	Denominator degrees of freedom for the type III test. DDF_T3 serves as a common prefix. The _XX suffix, appended to the prefix, indicates the specific variable(s) ( Sex or Age , for example) used in the analysis. When more than one variable is considered (the interaction of Sex by Age , for example) each variable is appended to the prefix as follows: DDF_T3_Sex_Age .
PrF_T3_ XX	Probability of the type III test = the p -value. PrF_T3 serves as a common prefix. The _XX suffix, appended to the prefix, indicates the specific variable(s) ( Sex or Age , for example) used in the analysis. When more than one variable is considered (the interaction of Sex by Age , for example) each variable is appended to the prefix as follows: PrF_T3_Sex_Age .