[BioC] GCRMA with HG-U95A and HG-U95Av2

James W. MacDonald jmacdon at med.umich.edu
Fri Dec 8 18:07:45 CET 2006

Nicolas STRANSKY wrote:
> Le 12/08/2006 05:19 PM, Seth Falcon a écrit :
>>>Has anybody been recently successful with a GCMRA normalization of
>>>both U95A and U95Av2 chips ?
>>You mean mixed together, right?
> Yes.
>>I don't have experience with that so don't have any advice.  But
>>normalizing one or the other should worth as documented.
> I am aware that it is possible to normalize one or the other and I have
> no problem with that... but problems occur when I try to normalize both
> types of chips at the same time, which should be possible as they only
> differ with a hundred probe sets.
Most likely these chips were run at different times, possibly in 
different labs. You might be better off computing expression values on 
each set separately, then subsetting to the intersecting probesets and 
fitting a mixed model. That would get around any need to combine the 
AffyBatches which appears to be a difficult task.



James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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