[BioC] GCRMA-induced correlations?

[Robert Gentleman]

Package developers are encouraged to include a NEWS file, either at the 
top level, or in the inst directory (not both), that contains such 
details.  The format should be similar to that of the NEWS file that 
comes with R.  The Biostrings package also has a nice example of such a 
file.



Richard Friedman wrote:
> 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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> 
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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
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org