Gene Set Enrichment

Running this process for the AffymetrixLatinSquare sample setting generates the tabbed Results window shown below. Refer to the Gene Set Enrichment 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:

Tab Viewer

This pane provides you with a space to view individual tabs within the Results window. Use the tabs to access and view the output plots and associated data sets.

The following tab is generated by this process:

•	ProbF Trt: This tab displays volcano plots of various F-tests for enrichment.

Drill Downs

Action buttons provide you with an easy way to drill down into your data. Selected the desired points and click one of the following action buttons:

•	Venn Diagram: Click Venn Diagram to launch a dialog from which you can select up to 5 categories and create a Venn diagram to display the overlap of those categories.

•	Contingency: Click Contingency to perform a Contingency Table analysis of selected categories.

•	Forest Plot: Click Forest Plot to display a Forest Plot of the selected categories.

•	Gene List: Click Gene List to display a list of the genes associated with the selected categories.

General

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

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

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

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