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

[Simon Anders]

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