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

[Naomi Altman]

There should not be a problem as long as you have read counts for 
each exon.  The main issue is that you have little power if the 
number of reads for a feature is small.  So you will need high 
coverage.  You might want to use a normalization method such as the 
quantile method in edgeR, as I am not sure the others have been 
tested for this type of data.  (

--Naomi

At 02:18 PM 3/31/2011, adeonari at mrc-lmb.cam.ac.uk wrote:
>Hello Bioconductor community,
>
>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!
>
>Cheers,
>
>Andrew
>
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