[BioC] GCRMA-induced correlations?
rgentlem at fhcrc.org
Tue Feb 19 22:31:01 CET 2008
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Richard Friedman wrote:
> Is there a mechanism to let us know when the version with
> this change has been released and that it contains the change?
> For example, let us say that I update GCRMA from the
> current version, automatically. Will it say in the Vignette or
> somewhere that
> the change has indeed been made?
> Please excuse my ignorance if there is some standard
> mechanism of which I am not aware.
> Thanks and best wishes,
> Richard A. Friedman, PhD
> 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
> "Sure I am willing to stop watching television
> to get a better education."
> -Rose Friedman, age 11
> On Feb 19, 2008, at 3:36 PM, Zhijin Wu wrote:
>> Yes, to eliminate this artifact The truncated values will no longer be
>> adjusted in the next release of GCRMA.
>> Jenny Drnevich wrote:
>>> Hi Zhijin,
>>> A client pointed out a July 2007 article by Lim et al. testing
>>> normalization/pre-processing methods for their effects on pairwise
>>> correlations between probesets (Bioinformatics 2007 23(13):i282-i288;
>>> doi:10.1093/bioinformatics/btm201; full link below). They reported
>>> GCRMA introduced severe artificial correlations between probesets;
>>> looked for a cause and think it's due truncation of low-intensity
>>> after Non-Specific Binding adjustment and then the Gene-Specific
>>> adjustment on these truncated values. They also tested a specific
>>> correction to the GCRMA algorithm that appears to prevent the
>>> correlation and suggest that it become an option or even a default in
>>> the R implementation of GCRMA.
>>> What do you think of this article? Are there any plans to implement
>>> their suggestion?
>>> Comparative analysis of microarray normalization procedures:
>>> effects on
>>> reverse engineering gene networks
>>> Jenny Drnevich, Ph.D.
>>> Functional Genomics Bioinformatics Specialist
>>> W.M. Keck Center for Comparative and Functional Genomics
>>> Roy J. Carver Biotechnology Center
>>> University of Illinois, Urbana-Champaign
>>> 330 ERML
>>> 1201 W. Gregory Dr.
>>> Urbana, IL 61801
>>> ph: 217-244-7355
>>> fax: 217-265-5066
>>> e-mail: drnevich at uiuc.edu
>> Zhijin (Jean) Wu
>> Assistant Professor of Biostatistics
>> Brown University, Box G-S121
>> Providence, RI 02912
>> Tel: 401 863 1230
>> Fax: 401 863 9182
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
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rgentlem at fhcrc.org
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