Dear all,
please could I have your advise on the following : shall we have multiple samples from ChIP experiments (where the proteins A, B, C were immuno-precipitated on the chromatin) and INPUT DNA (from the samples A, B, and C), would we normalize them all together (i.e. ChIP + INPUT) in edgeR, for example ? Many thanks.
-- bogdan
If you haven't already, you should check out the csaw package, both the User's Guide and the associated publication.
Dear Ryan, thank you for your reply. Here the question is not very much about TMM normalization (implemented in csaw or edgeR); I would be interested to know whether I could normalize in the same procedure both ChIP samples and INPUT_DNA samples. Sorry if I missed the discussion in the manual. Any suggestions are welcome.