[BioC] Using DESeq or EdgeR for Exon Differential Expression Analysis

[adeonari at mrc-lmb.cam.ac.uk]

Hello Simon, Wei, Naomi, Davis,

Thanks for your input, I suspected the exon length could be a potential
issue. Look forward to your coming work on this Simon!

Cheers,

Andrew

> Hi Andrew
>
> On 03/31/2011 08:18 PM, adeonari at mrc-lmb.cam.ac.uk wrote:
>> We were wondering if it would be possible to perform differential
>> expression analysis of exon expression using DESeq or EdgeR. Would the
>> statistical assumptions be the same, and has anyone attempted this type
>> of
>> analysis? Any feedback or insights would be really appreciated!
>
> As others already remarked: You can simply consider each exon as an
> individual unit and study it independently from the other exons in the
> gene. If a gene is differentially expressed, you should see a
> significant change for all those of its exons that are long enough to
> have attracted enough counts to achieve significance. However, if you
> want to see alternative splicing regulation, this might not help to
> much, as you will need to tease apart the changes in overall gene
> expression from those that are only affecting the exon under
> consideration. We are currently working on such a method.
>
>    Simon
>
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