[BioC] Replicates array

[Paola Sgado']

Hi,
I didn't explain the things properly, sorry!

What I have is three different treatments, each one with its own 
control. Of these 6 chips I have three duplicates done in two different 
places. At the end what I compare is treated vs untreated, so I can 
have list of differentially expressed genes without considering the 
replicates. My question is: Do I need to process (rma) all the chips 
together to be able to compare the replicates? Does it change the list 
of differentially expressed genes if I do separate rma for the 
different replicates?

Thanks again for your help
Paola