Hi, I have a set of affymetrix data which includes three groups. I would like once to run supervised analysis by performing all three pairwise comarisons and once unsupersied by clustering samples. The question is: Should I run the clustring on the normalized observed data (one that comaes out of RMA) or on coefficients after fitting in order that the input for the two type of analysis would be comparable? Having the following experimental design: A B C Array1 1 0 0 Array2 1 0 0 Array3 0 1 0 Array4 0 1 0 Array5 0 0 1 Array6 0 0 1 like in second design of chapter 13 "Two Groups: Affymetrix", is the coefficients after lmFit(data,design) are the same as the data itself? Thanks, Ron