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.

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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