[BioC] chips A,B and C

[Antille,Nicolas,LAUSANNE,NRC-BAS]

I'm currently working on an experiment involving chips MG_U74Av2,
MG_U74Bv2 and MG_U74Cv2. The RMA normalization treats every
types of chips separately (only one .CDF file is required). Thus, I
need to perform RMA three times and the result is certainly  
different from the one I would obtained performing RMA on all
data simultaneously (especially for quantile normalization).

Has someone already meet this problem? Are the results between
the two methodolgies very different? More generally, do we observe
differences between chips A, B and C (expression level, variability,...)?

Thank you very much for your response!

Regards

Nicolas