Hello,
When using DESeq2, does it matter the order of the groups of samples we feed to this package?
From some preliminary test runs, if I test Group1 against Group2, and then Group2 against Group1, I can see that the base means are the same for all genes, but the log2FoldChange has its sign inverted. This behavior makes sense to me, but I would like to know the mathematical/statistical rationale for this outcome using this package.
Thanks,
Marcelo
Additionally, you asked if anything else should change, and the answer is no: swapping the groups should only change the sign of the LFC.