[BioC] normalization question (conceptual)

[James W. MacDonald]

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).

In most cases it is preferable to normalize all of your samples 
together, and I don't see any compelling reason to do things separately 
here.

I would bet that the error you received was something like 'Unable to 
allocate a vector of XXXX Mb', which implies that you ran out of memory. 
A reasonable workaround is to use justRMA().

Jim


> 
> 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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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623