[BioC] GCRMA Normalization Differences between Windows and MAC

Zhijin Wu zwu at stat.brown.edu
Thu Mar 25 13:58:49 CET 2010

We did make changes of the package over the years. One of the major 
changes is in the step of "gene specific binding (GSB) adjustment". This 
adjustment is done because probes have different efficiency in 
hybridization. At the background adjustment step, we do not really give 
probes 0 even if they appear to be mostly background, because of the 
trouble for log transformation. So those probes were shrunk to a lower 
bound parameter instead of 0. The original GSB adjustment was done on 
all probes. later we have decided to leave those probes at the lower 
bound un-adjusted because these were most likely background only (Thanks 
to  Lim et al, who discovered the problem and suggested the fix. see 
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i282 .)

This change would mostly affect genes that are probably not expressed, 
but would also affect some genes that have a few very weak probes.

martin martinez wrote:
> I am performing a gene expression analysis and I founded important
> differences between the results of the GCRMA normalization obtained in a
> Windows machine (gcrma ver.2.16) and a MAC one (gcrma ver.2.18.1). It
> consists in a cut off, so all the lower values dissapear. The code is next:
> library(affy)
> library(gcrma)
> affy.data= ReadAffy()
> eset.gcrma=justGCRMA() (the same as eset.gcrmax=gcrma(affy.data))
> my question is about default values. Does them variate between versions? The
> difference is very significant and I tried changing all the arguments, but
> not satisfactory results are obtained.
> Regards,
>   Martín M.
> 	[[alternative HTML version deleted]]
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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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