[BioC] Merging 2 groups of samples

[rgentlem]

yep, mixed effects models, see our technical report at:
http://www.bepress.com/bioconductor/
on synthesizing microarray experiments. The best advice I can give is to 
not jointly normalize (treat them seperately and use a random effect 
term for the experiment). Your problem is a bit easier since you don't 
need to worry about matching probes

there is a package which needs to appear somewhere, but I think has not 
yet done so

  Robert


Lana Schaffer wrote:
> Bioconductor users,
> We have two groups of samples on HU133plus2 chips done 1 year apart.
> After I normalized with RMA,  the two groups are clustering into separate
> clusters at a low level of correlation.
> Can someone suggest a way to analyze these samples together?
> 
> Lana Schaffer
> Biostatistics/Informatics
> The Scripps Research Institute
> DNA Array Core Facility
> La Jolla, CA 92037
> (858) 784-2263
> (858) 784-2994
> schaffer at scripps.edu
> 
> 
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org