[BioC] normalization question (conceptual)

[Paul Mack]

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 -- actually a timecourse of 4 post-treatment intervals (0, 3, 6, 
and 24 hrs later) -- 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 4 time 
intervals. 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 time interval. 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)? If so, is there a recommended way to do so? I attempted 
to normalize all my arrays at once in R but received an error message 
(which I unfortunately did not save).

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