[BioC] Has GCRMA version 2.12 been benchmarked

[Richard Friedman]

Zhijin,

	Thank you for your reply.
	One more question.
	Has GCRMA version 2.12 been benchmarked for accuracy?
	That is to say is it as accurate as version 2.10 for differential  
expression?

Best wishes,
Rich

On Jul 8, 2008, at 12:22 PM, Zhijin Wu wrote:

> 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
>>
>>
>>
>