[BioC] LIMMA and Clustering

[Ron Ophir]

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