[BioC] Differential expression analysis of DESeq

[Wolfgang Huber]

Sean Davis scripsit 08/18/2011 03:38 PM:
> On Thu, Aug 18, 2011 at 9:23 AM, geng chen<chengeng66666 at gmail.com>  wrote:
>> Dear Sir/Madam,
>>
>> I have read the paper of DESeq, it seems mainly be used for detecting
>> differential expression genes. Could I use the same methods as genes to
>> calculate the differential expression of isoforms? Thank you very much.
>
> You could check out the DEXSeq package, also.
>
> Sean

Dear Geng Chen

Yes. Note that DEXSeq

1. finds those genes in which isoforms are differentially expressed

2. within those genes, tries to determine which exons are affected in 
particular. This works well for genes with many exons, where the 
differential expression only affects a few exons.

DEXSeq does not attempt to solve the isoform deconvolution problem.

Best wishes
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber