[BioC] normalization

[Paul Mack]

Dear Bioconductor:

I have a question concerning normalization of data from Affymetrix 
Drosophila chip .cel files. This is a general question about how to 
normalize over multiple treatments. I have data from multiple (4) 
treatments with 3-6 biologically independent arrays for each treatment. I 
also have 5 biologically independent control arrays -- the same 5 arrays 
serve as controls for comparison to each of the treatments. I have used RMA 
to compare each treatment separately against the controls to determine 
genes whose expression levels change significantly under each treatment. As 
a result, I normalized each of the four treatments to the controls 
separately -- that is I did four separate normalizations with the one set 
of controls and one set of treatment arrays. Would it be more appropriate 
to normalize all of the the experimental arrays in the analysis to the 
controls at once rather than separately, one treatment at a time (as 
described above)?

Many thanks.

Paul Mack, Ph.D
Department of Genetics
University of Georgia
Athens, GA
USA

706-542-1578 (w)
706-542-3910 (fax)
paulmack at arches.uga.edu