Hi,


On Friday, February 1, 2013, Fong Chun Chan wrote:

> Hi,
>
> This is somewhat of a odd request to run DESeq. Basically, I am interested
> finding whether a single gene is differentially expressed between two
> groups of RNA-seq libraries. I could run DESeq just to get the differential
> expression of that one gene. But that seems to be computationally expensive
> just to find whether a single gene is differentially expressed.


Have you tried doing it on all of your data? I suspect it won't take much
time at all.

Is there another reason that you want to be blind to the rest of the
changes that are happening in your data?



> I understand that DESeq needs to estimateSizeFactors() and
> estimateDispersions() on the entire library using all the reads. But is
> there a way in the nbinomTest() to just restrict the analyses to just one
> gene? One way I was thinking was to create another CountDataSet with just
> that one gene, and then fill in the slots of sizeFactors and DIspersions
> with the data from the whole CountDataSet.
>
> Has anyone else tried to do this?
>
> Thanks,
>
> Fong
>
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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