Question: Deseq2 for down stream analysis
5.0 years ago by
Fabrice Tourre • 970
Fabrice Tourre • 970 wrote:
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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