I have a couple of questions about DESeq2:
in the DESeq2 workflow, to test the dex treatment effect, the following command was used:
dds <- DESeqDataSet(se, design = ~ cell + dex)
And I guess the only factor here is "dex" and it might be more straightforward to use:
dds <- DESeqDataSet(se, design = ~ dex)
If I am performing an ANOVA-like comparison of 3 groups A, B and C:
design(dds) = ~ group dds = DESeq(dds, test = "LRT", reduced = ~ 1) results(dds)
To extract the DE genes between B-vs-A and C-vs-B. We should use the following commands and no post-hoc tests are needed. Is it correct?
res.B.vs.A <-results(dds, contrast=c("group","A","B")) res.C.vs.B <-results(dds, contrast=c("group","B","C"))
Many thanks for Michael Love and colleagues for contributing such an excellent software and their answers in the forum!