[BioC] Improvements on GCRMA function

Richard Friedman friedman at cancercenter.columbia.edu
Mon Feb 1 16:30:34 CET 2010

Dear Javier,

On Feb 1, 2010, at 10:24 AM, Javier Pérez Florido wrote:

> Dear list,
> Some months ago, I read the following paper:
> http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i282
> It is said:"we identify a crucial step in GCRMA responsible for  
> introducing severe artifacts in the data leading to a systematic  
> overestimate of pairwise correlation. This has key implications not  
> only for reverse engineering but also for other methods, such as  
> hierarchical clustering, relying on accurate measurements of  
> pairwise expression profile correlation. We propose an alternative  
> implementation to eliminate such side effect".
> I've checked the papers that reference this work, but no one is  
> about the improvement of GCRMA. Does anyone know if, after this  
> paper was published, GCRMA was fixed?
> Thanks,
> Javier
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I believe that it was fixed in most recent versions.

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)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu

In Memoriam,
Patrick McGoohan

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