Dear bioconductor list,

I have a question concerning RMA-normalization:

There are for example 200 CEL-Files and the clinicians have several
research questions - each concernig only a subset of the 200 samples
including the possibility that some samples are included in more than
one question.

There are two possibilities to normalize the CEL-Files: 

1.: Read all 200 chips in an affybatch-object and normalize all 200
chips together and further analyze the required subset. 

2.: Read only the required chips in an affybatch-object, normalize these
chips and then perform further analysis    
I think that this approach is the better one but it has the disadvantage
that some samples are included in several normalizations ending in
different gene expression levels for a single sample.

What is (from a statisticians view) the appropriate approach to
normalize CEL-Files in this case?

Thank you in advance
Sylvia 




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