I was wondering how dexseq is calculating the differential exon usage. I am having troubles interpreting the results, which I think are significant, but dexseq does not :-)
I have here one of the genes from my run, which looks to me, that it is very much differentially used. the three plots are the results for the counts, the expression and the splicing events calculated by DEXSeq.
I don't understand the results. To my eyes, it looks as if the counts of exons 26-60 should be differentially expressed, but somehow they're not. On the other hand, the two exon defined as different are exons 17 and 19, which doesn't look at all changed.
splicing: here it looks completely different than the other two plots.
Is there an explanation to that?