Deseq2 for down stream analysis
Fabrice Tourre <[email protected]>
| Newsgroups | gmane.science.biology.informatics.conductor |
|---|---|
| Message-ID | <CAN31xkepWbT2kj-=C7aTFN7u-0c9Own0Rq3D3b5+Xtjvkci4ng@mail.gmail.com> |
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. _______________________________________________ Bioconductor mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor