[BioC] Deseq2 for down stream analysis

Fabrice Tourre fabrice.ciup at gmail.com
Sun Aug 10 14:27:15 CEST 2014

Dear expert,

I've been using DESeq for my RNA-Seq differential expression analysis.
Now I want to do GSEA. I have got follow expression value. which one
should I used for the down stream analysis? rc, rld or vsd?

rc <- counts(dds)
rld <- rlog(dds)
vsd <- varianceStabilizingTransformation(dds)
rlogMat <- assay(rld)
vstMat <- assay(vsd)

Then I want to use the DESeq result to generate a ranked-list, which
will be used as the input in GSEA. My question is: Should I rank the
genes using the fold changes or using the q-values?

Thank you very much in advance.

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