[BioC] GCRMA-induced correlations?

[Richard Friedman]

Zhijin,

	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,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
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/

"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  
>> different
>> 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  
>> that
>> GCRMA introduced severe artificial correlations between probesets;  
>> they
>> looked for a cause and think it's due truncation of low-intensity  
>> values
>> after Non-Specific Binding adjustment and then the Gene-Specific  
>> Binding
>> adjustment on these truncated values. They also tested a specific
>> correction to the GCRMA algorithm that appears to prevent the  
>> artificial
>> 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?
>>
>> Thanks,
>> Jenny
>>
>> Comparative analysis of microarray normalization procedures:  
>> effects on
>> reverse engineering gene networks
>>
>> http://bioinformatics.oxfordjournals.org/cgi/content/full/23/13/ 
>> i282? 
>> maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&andorexacttitle=and&andorex 
>> acttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortsp 
>> ec=relevance&volume=23&firstpage=i282&resourcetype=HWCIT&eaf
>>
>>
>>
>> <http://bioinformatics.oxfordjournals.org/cgi/content/full/23/13/ 
>> i282? 
>> maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&andorexacttitle=and&andorex 
>> acttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortsp 
>> ec=relevance&volume=23&firstpage=i282&resourcetype=HWCIT&eaf>
>>
>> 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
>> USA
>>
>> 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
> http://stat.brown.edu/~zwu
>
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