[BioC] Replicates array

[Paola Sgado']

Hi
I just started to work with oligonucleotide microarray and I would like 
to have suggestions on the methods I should use to analyse the data.

I have three duplicates done in two different places, so they look very 
different in terms of background and signal intensities. Since I'm not 
going to have more duplicates I would like to get the most information 
possible from these, even if I do know that it is not the perfect 
experimental design!

My question is, if the chips are very different, should I normalize 
them separately (for example make to groups)? Does it make sense to 
compare them between two gruops if they are normalised separately? 
Should I just compare the differentially expressed genes lists coming 
from the two different group of duplicates??

Thank you for your help!!
Paola