hi, 

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.

counts:

expression:

splicing: here it looks completely different than the other two plots.

Is there an explanation to that?

thanks

Assa

Hi Assa,

DEXSeq doesn't look for differential expression. The tool is designed to look for a differential usage of single exon bins compared to the usage of all other exon bins in a gene. In your case the gene shows an over expression in EB2 compared to the other condition. Hence the high expression in EB2 is normal, except for the two exon bins 17 and 19. Here expression/usage is not on the same level as compared to the other exons. That's why they are marked as significant. The concept of usage is completely different to expression and takes a while to wrap one's head around it. Actually here, DEXSeq Usage and Expression Confusion is a very good example, explained by Simon Anders. That should make things quite clear

best

mathias