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

[Davis McCarthy]

Hi there

Assuming you are talking about RNA-Seq data then differential expression analysis of exon expression can certainly be done using edgeR in the same fashion as if the counts were summarised at the gene level. The important thing is that you have raw counts for whatever features are of interest (whether genes, exons, methylation regions, etc.) as your input data for edgeR. The methods apply to count data generally, so DE analysis of exon expression can be done fine.

Cheers
Davis


On Apr 1, 2011, at 7:27 AM, vasu punj wrote:

> You are asking about Affy Exon Expression array or after RNA-seq?
>  
> Vasu
> 
> --- On Thu, 3/31/11, adeonari at mrc-lmb.cam.ac.uk <adeonari at mrc-lmb.cam.ac.uk> wrote:
> 
> 
> From: adeonari at mrc-lmb.cam.ac.uk <adeonari at mrc-lmb.cam.ac.uk>
> Subject: [BioC] Using DESeq or EdgeR for Exon Differential Expression Analysis
> To: "'bioconductor at r-project.org'" <bioconductor at r-project.org>
> Date: Thursday, March 31, 2011, 1:18 PM
> 
> 
> 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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------------------------------------------------------------------------
Davis J McCarthy
Research Technician
Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Vic 3052, Australia
dmccarthy at wehi.edu.au
http://www.wehi.edu.au




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