[BioC] GCRMA-induced correlations?

[Zhijin Wu]

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&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=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&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=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