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

[Zhijin Wu]

Yes, the 2.12 version has made the change so probes without affinity 
information do not go through GSB(gene specific binding) adjustment.  So 
there may be a small number of probesets that are affected.

best
Zhijin
 Richard Friedman wrote:
> 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,
> Rich
> ------------------------------------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> 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
> http://cancercenter.columbia.edu/~friedman/
>
> In Memoriam,
> Algirdas Jonas Budrys
>
>
>