Output Description

Allele Specific Expression Filter

Running this process for the pseudo_rna sample setting generates one filtered output data set accessed from a Results window shown below. Refer to the Allele Specific Expression Filter process description for more information about this process.

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 tabs are generated by this process:

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Volcano Plot: This tab shows a Mean Square Error Volcano Plot .

The output data set (identified by the appended _asf suffix) corresponding to this plot can be accessed by selecting View Data.

Log Ratio DNA versus Log Ratio RNA Plots , either for selected SNPs or all significant SNPs, can be displayed using the Display button. A representative example of two of the plots is shown below.

Each plot in the Log Ratio Plots represents an individual locus. Homozygotes for the two alleles in each plot are circled, heterozygotes are indicated by black arrows. The red solid lines represent the fitted regression lines for homozygotes. The dashed lines to either side represent the 95% confidence bands.

The plot on the left shows that for this SNP, heterozygotes cluster within or close to the regression line and show ratios that are intermediate between the homozygotes. This indicates a lack of allele-specific expression.

The plot on the right shows that heterozygotes lie well outside of the confidence bands indicating allele-specific expression.

Finally, the -log10 p-value reference can be adjusted and the significance recomputed for all tests.

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.