Sorry for such a basic question, but I got confused. As far as I know, the RMA method implemented in affy package is a standard method for microarray data normalization. Could you let me know if the main code
data.rma.norm = rma(raw.data) normalize data in three stages, background correction, quantile normalization, and log2 transformation? So the output of the above code is log2 expression value, yes? or there is another story?