[BioC] normalization question (conceptual)

[Naomi Altman]

This question comes up at least monthly on this list.  You can use the 
"searchable e-mail archive" to look at previous discussion.

In summary, arrays that are to be analyzed together for differential 
expression or clustering should be normalized together.

--Naomi

At 09:01 AM 2/22/2005, Paul Mack wrote:
>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
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111