Hi!

In Deseq2 it has to be set which is control and which is treatment. Let's say I have 2 treatments - A and B and I run analysis so that A is control. If I now run the analysis again so that B is control and A treatment, would that change my result statistics or would just the up-regulated become down-regulated and vice versa?

Thanks!

I moved this to an answer, since it's the answer.