[BioC] interpreting DEXSeq output

[Elena Sorokin]

Hi Alejandro,
Yes, the merged genes I find are difficult to interpret - because the 
differential exon usage is probably just differences in total gene 
expression. I still wonder about it, because in my mapping procedure, I 
do a very stringent alignment where reads that map to more than one 
place in the transcriptome get thrown out of the BAM file. However, I 
would say this only affects less than 1 in 10 of my differential exon 
results, so I believe I can work around it. I did use the plot function, 
and it's very helpful.
Thanks and best wishes,
Elena

On 6/19/2012 3:29 AM, Alejandro Reyes wrote:
> 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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>