Alternative splicing results in a single gene coding for multiple protein isoforms, so this task can only be invoked from transcript level data. The algorithm is is based on ANOVA to detect genes with multiple transcripts showing expression changes differently in different biology groups, e.g. a gene has two transcripts: A and B,  transcript A is showing up-regulation in treated group comparing to control group, and B is showing down regulation in treated group.

Alt-splicing ANOVA dialog

The alt-splicing dialog is very similar to ANOVA dialog, the analysis is based on the ANOVA model specified. To setup ANOVA model, select factors from sample attributes. The factors can be categorical or numeric attribute(s). Click on a check button to select and click Add factors button to add it to the model (Figure 1).

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