Dear all,

I am a edgeR user and I would like to know if edgeR reports 'average' cpm for each of the conditions tested in the analysis. Having a look at the output it seems the only information I have is the 'average' log(cpm) calculated using all the libraries. So the question would be, is there any way to output 'average' cpm (condition 1) and 'average' cpm (condition 2) for each tag ?

Thanks for clarifying me this point.

AEC.

Dear AEC,

You could get average cpm for each group in several ways. You could subset the DGEList by group and compute aveLogCPM() on each subset. Or you could fit a linear model with a coefficient for each group, then the fit$coefficients hold the aveLogCPM for each group.

Best wishes
Gordon