[BioC] LARGE Change in GCRMA expression values between versions (REPEAT QUESTION: PLEASE REPLY)

Richard Friedman friedman at cancercenter.columbia.edu
Tue Jul 8 17:10:20 CEST 2008

Dear Zhijin,

	(I sent the following in May and  June to the list (worded slightly  
differently) but did not receive a reply.
  I would appreciate it if you, or someone on the list could  could  
clear up this problem)

	I am noticing a large change in the absolute values of
intensity measurements

	For the same probeset and and array normalized with the same 8 other
arrays done with
GCRMA 2.10 I got 5.27
but for
GCRMA 2.12  I got 3.14

Does this sound like a change that can be expected between versions
2.10 and 2.12, or does it sound as if I had made an error of some kind?

Is the change due to revising GCRMA to take the criticism  of Lim et  
al. into account?
Is so has version 2.12 been benchmarked against affycomp?

Thanks and best wishes,
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu

In Memoriam,
Algirdas Jonas Budrys

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