[BioC] RMA normalization when using subsets of samples

[Wolfgang Huber]

Dear Sylvia,

this might not be the answer that you want to hear, but for the end 
result it should not matter (substantially) which of the two 
possibilities you take, and I would be worried if it did.

Best wishes
  Wolfgang

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Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber
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Sylvia.Merk at ukmuenster.de wrote:
> 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 
>