[BioC] Linear models with different platforms

[Robert Gentleman]

have a look at the Bioconductor report series
   http://www.bepress.com/bioconductor/
(other contributions are welcome)

for the paper on the Synthesis of Microarray experiments, which gives 
some details on fitting mixed effects models (which is sort of what you 
are asking about). Code etc is available in the GeneMetaEx package
  at
   http://www.bioconductor.org/pub/genemetaex

best wishes
   Robert


Sean Davis wrote:
> I have a pretty interesting dataset that involves three phenotypes
> (tumor/normal/cell line) on two different array platforms (quite different).
> I am interested in fitting a linear model but I do not want to assume that
> the variance on the two different platforms is the same (it is clearly not).
> The samples are all biological replicates.  Any suggestions?
> 
> Thanks,
> Sean
> 
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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