[BioC] interpreting DEXSeq output

[Alejandro Reyes]

Dear Elena,

Thanks for your email! The reason that multiple genes are merged into a 
single one is because they share exons, and it is not obvious to assign 
this exon to a single gene.  You can see more in detail if you do a 
"plotDEXSeq" displaying the transcripts.  So far, I have not seen a big 
problem on it but I can imagine a situation in which the merged genes 
are differentially expressed: there would be differences in exon usage 
that are differential expression in reality...

Is it introducing messy results for you?

Alejandro


> Hello,
>
> How should we be interpreting output from DEXSeq in which some geneIDs 
> within the DEU results table are denoted by multiple genes separated 
> by + signs? I can send examples of what I mean to the developers, if 
> my question is unclear.
>
> Especially when the architecture of the two or even three genes is 
> quite different, this  type of output perplexes me. Sorry if my post 
> was answered elsewhere!
>
> Best wishes,
> Elena
>
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