Variance Components

Running this process using the Merlin_asp sample setting generates the tabbed Results window shown below. Refer to the Variance Components 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.

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.

•	Summary Chart : When there are multiple annotation groups ( chromosomes or genes, for example), this tab displays the number of significant markers in each annotation group for each test.

•	Manhattan Plot : When there are multiple annotation groups (chromosomes or genes, for example), this tab displays a scatter plot of the p-values across all annotation groups.

•	Annotation Group Results : When there are multiple annotation groups (chromosomes or genes, for example), a separate Results tab with an overlay plot of p -value by chromosome location is created for each annotation group. In this example, there are no annotation groups specified.

•	All P-Value Plots : When there are multiple annotation groups (chromosomes or genes, for example), the All P-Value Plots tab shows all the p -value plots from the Annotation Group Results tabs in a single display.

Note : When an annotation group variable is not specified, as in this example, or there is only one annotation group, the tab is named P-Value Plot and contains an overlay plot of p -value by chromosome location for all markers.

•	SAS Output : This tab displays the SAS output from running PROC MIXED to fit the variance components model, including one with the null model including covariates only then a run of PROC MIXED for each marker for the alternative model.

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:

•	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.

•	UniGene Database : Select points or rows and click UniGene Database to access information from the Unigene database for selected genes or markers

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

•	dbSNP : Select points or rows and click dbSNP to open a browser window directed to an NCBI dbSNP search for the pair of SNPs associated with the particular instance of this button.

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.