Hi, I'm trying to normalize HG-U95A and HG-U95Av2 chips with GCRMA. I have tried two methods that were described on this list but have been unsuccessful with both. The first one was proposed by Zhijin Wu and adapted by Vincent Detours (http://article.gmane.org/gmane.science.biology.informatics.conductor/ 2747/). It involved combineAffyBatch. I could not get it to work, it always ends up with the following error: > affinity.info1=compute.affinities("hgu95a") Computing affinities.Done. > affinity.info1=new("AffyBatch",exprs=exprs(affinity.info1),cdfName=cdf Name(affinity.info1),nrow=640,ncol=640) > affinity.info2=compute.affinities("hgu95av2") Computing affinities.Done. > affinity.info2=new("AffyBatch",exprs=exprs(affinity.info2),cdfName=cdf Name(affinity.info2),nrow=640,ncol=640) > affinity.mix12=combineAffyBatch(list(affinity.info1,affinity.info2), c("hgu95aprobe","hgu95av2probe"), "hgu95av12new") package:hgu95aprobe hgu95aprobe package:hgu95av2probe hgu95av2probe 197193 unique probes in common Error in "dimnames<-.data.frame"(`*tmp*`, value = list(c("Batch 1: ", : invalid 'dimnames' given for data frame The second solution involves the packages created by Ben Bolstad (http://bmbolstad.com/misc/mixtureCDF/MixtureCDF.html) and the sample R code from http://bmbolstad.com/misc/mixtureCDF/mixtureCDFexample.R. > My.version1<- ReadAffy(celfile.path="./A") > My.version2<- ReadAffy(celfile.path="./Av2") > my.merged <- merge.mix(My.version1,My.version2,mergecdfName="HGU95A_V12mix") > gcrma(my.merged) Attaching package: 'hgu95av12mixcdf' Adjusting for optical effect..............................Done. Computing affinities[1] "Checking to see if your internet connection works..." Error in getProbePackage(probepackagename) : You do not have write access to /usr/local/lib/R/site-library Please check your permissions or provide a different 'lib' parameter. In order to correct this error, I have tried to apply so solution described here: http://article.gmane.org/gmane.science.biology.informatics.conductor/6 012 But the package I create is not installable for an unknown reason. # R CMD INSTALL /tmp/hgu95av12mixprobe_1.14.0.tar.gz * Installing *source* package 'hgu95av12mixprobe' ... ** R ** data ** help >>> Building/Updating help pages for package 'hgu95av12mixprobe' Formats: text html latex example hgu95av12mixprobe text html latex example ** building package indices ... Error in load(zfile, envir = envir) : ReadItem: unknown type 101 Execution halted ERROR: installing package indices failed ** Removing '/usr/local/lib/R/site-library/hgu95av12mixprobe' So has anybody been successful for a GCMRA normalization with U95A and U95Av2 chips ? Thanks for any help, -- Nicolas STRANSKY ?quipe Oncologie Mol?culaire http://www.curie.fr/equipe/301 Institut Curie - UMR 144 - CNRS Tel : +33 1 42 34 63 40 26, rue d'Ulm - 75248 Paris Cedex 5 - FRANCE Fax : +33 1 42 34 63 49

Nicolas STRANSKY <nico at="" stransky.cx=""> writes: > Le 12/05/2006 07:01 PM, Nicolas STRANSKY a ?crit : > > Hello, > >> I'm trying to normalize HG-U95A and HG-U95Av2 chips with GCRMA. I >> have tried two methods that were described on this list but have been >> unsuccessful with both. > > Has anybody been recently successful with a GCMRA normalization of both > U95A and U95Av2 chips ? You mean mixed together, right? I don't have experience with that so don't have any advice. But normalizing one or the other should worth as documented. + seth

Le 12/05/2006 07:01 PM, Nicolas STRANSKY a ?crit : Hello, > I'm trying to normalize HG-U95A and HG-U95Av2 chips with GCRMA. I > have tried two methods that were described on this list but have been > unsuccessful with both. Has anybody been recently successful with a GCMRA normalization of both U95A and U95Av2 chips ? -- Nicolas STRANSKY ?quipe Oncologie Mol?culaire http://www.curie.fr/equipe/301 Institut Curie - UMR 144 - CNRS Tel : +33 1 42 34 63 40 26, rue d'Ulm - 75248 Paris Cedex 5 - FRANCE Fax : +33 1 42 34 63 49