Dexseq - Condition / Group Level Average Of Exon Expression

Question

[mengqingying]

I am using DEXSeq to find deferentially expressed exons. But I wonder except for the statistics, is it possible to calculate the average/mean of the exon expressions in each condition/groups? If true, how?

Thanks!

Answer 1

[Devon Ryan]

The counts() function can take an ExonCountSet object and return the raw or normalized counts. The easiest thing to do, then, would be to c <- counts(ecs, normalized=T) and then just apply(c, 1,...) appropriately on the results.

Edit: I should have browsed SEQanswers first. Apparently this is even easier to do with estimatelog2FoldChanges (presumably `getOnlyEffects=T). I'd never noticed that option before!