Dear users, I would like to draw your attention on a recent paper by Lim et al (Bioinformatics, 2007): "Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks" Bioinformatics 2007 23(13):i282-i288; doi:10.1093/bioinformatics/btm201 http://bioinformatics.oxfordjournals.org/cgi/content/full/23/13/i282 This paper raises important concerns regarding GCRMA. In particular, they suggest that GCRMA induces artificial correlations between probe sets with small expression levels. They claim these correlations are induced by the Gene Specific Binding (GSB) adjustment step of GCRMA. My first question is: does anyone have a similar experience with GCRMA ? To our knowledge, this GSB adjustment step is not described in the original paper by Wu at al (A model-based background adjustment for oligonucleotide expression arrays, 2004, JASA). Does anyone know where it is described ? However, as mentioned by Lim, this step is (or can be) performed in the gcrma package . It is optional when the gcrma function is used (performed iff GSB.adjust=TRUE), but in justGCRMA this adjustment is systematically performed. Lim have proposed a reimplementation of this step where "uninformative probes" are not GSB-adjusted. Could it be included is an option in gcrma ? Any hints on these questions would be much appreciated. Regards, Pierre Neuvial.

Yes I am planning to include that modification of gcrma so uninformative probes will no longer be adjusted. Wolfgang Huber has pointed this out to me and it's underway. Pierre Neuvial wrote: > Dear users, > > I would like to draw your attention on a recent paper by Lim et al (Bioinformatics, 2007): "Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks" > > Bioinformatics 2007 23(13):i282-i288; doi:10.1093/bioinformatics/btm201 > http://bioinformatics.oxfordjournals.org/cgi/content/full/23/13/i282 > > This paper raises important concerns regarding GCRMA. In particular, they suggest that GCRMA induces artificial correlations between probe sets with small expression levels. They claim these correlations are induced by the Gene Specific Binding (GSB) adjustment step of GCRMA. My first question is: does anyone have a similar experience with GCRMA ? > > To our knowledge, this GSB adjustment step is not described in the original paper by Wu at al (A model-based background adjustment for oligonucleotide expression arrays, 2004, JASA). Does anyone know where it is described ? > > However, as mentioned by Lim, this step is (or can be) performed in the gcrma package . It is optional when the gcrma function is used (performed iff GSB.adjust=TRUE), but in justGCRMA this adjustment is systematically performed. Lim have proposed a reimplementation of this step where "uninformative probes" are not GSB-adjusted. Could it be included is an option in gcrma ? > > Any hints on these questions would be much appreciated. > > Regards, > > Pierre Neuvial. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- ------------------------------------------- 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