[BioC] RMA normalization, which samples should be normalized together

[Dipl.-Ing. Johannes Rainer]

hi,
we are interested in the response of patients to a special treatment, 
so we have patient samples before and after treatment. i have 
normalized this samples in different ways using RMA. As RMA tries to 
detect and correct probe effects by looking at the expresison levels of 
the probes across all chips it is not surprising that the outcome of 
the analysis differs depending on which chips i normalize together.
It is clear that i have to normalize all patient samples together if i 
want to compare the expression values of the genes (lets say using 
statistical tests). i am also analyzing the chips using the 'old 
fashioned way' by using M and A values and i suppose it is not 
problematic at all to compare M values of lets say patient 1, 6 hours 
sample against 0 hours sample with those from patient 2, also 6 hours 
versus 0 hours where the chips from the two patients were NOT 
normalized together.

-now my question is if someone else has experience in what samples 
could and should be normalized together with RMA. I saw that ther are 
(big) differences in the regulation (M) values if i normalize two 
different patients together compared with the values that i get when i 
normalize only samples from the same patients together.

thanks in advance