[BioC] Affy normalization question

[Mark W Kimpel]

Not infrequently on this list the question arises as to how to perform 
RMA on a large number of CEL files. The simple answer, of course, is to 
use "justRMA" or buy more RAM.

As I have learned more about the wet-lab side of microarray experiments 
it has come to my attention that there is a technical limitation in our 
lab as to how many chips can actually be run at one time and that there 
is a substantial batch effect between batches.

So, in my case at least, it seems to me that it would be incorrect to 
normalize 60 CEL files at once when in fact they have been run in 4 
batches of 16. Would it not be better to normalize them separately, 
within-batch, and then include a batch effect in an analytical model?

Is my situation unique or, in fact, is this the way most MA wet-labs are 
set up? If the latter is correct, should the recommendation not be to 
use justRMA on 80 CEL files if they have been run in batches?

Thanks,
Mark
-- 

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

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