16 months ago by
Zentrum für Molekularbiologie, Universität Heidelberg
No, of course not! Why would you think that?
(Background: The DESeq manual states, as explicitly as possible and since the very first version, that the matrix should contain "read counts", i.e., integer numbers that count how many reads map to the gene. Nevertheless, I have been asked hundreds of time various variations of: I have RPKM values. Can I use these, too? My data has been normalized and now it's no longer integer. Can I still use hem? I have done [insert arbitrary mathematics operation] to my counts. I can still input this to DESeq, right? etc.
So, please use DESeq on read counts and only on read counts. And take a moment to recall the meaning of the word "count". ;-)
Sorry for the rant; you just triggered with your question my sort-of-annual reminder to this site about this issue.)
As for your condition: Do you have paired samples, i.e., on tumour and one normal sample per patient? If so, you need to let DESeq know which samples belong to the same patient. Read up on "paired designs" in the manual.