Hi, similar to others (http://thread.gmane.org/gmane.science.biology.informatics.conductor/1 8693) I have to report an error with GCRMA (2.12.1). The other package I normally use ATM ("mouse4302") works fine in this setup. I also removed the mu11ksubacdf and mu11ksuba probes package and installed an older version (2.0.0) manually, but this also did not help. thank you very much, ido > raw <- ReadAffy(filenames=paste("cel/",pData(ad)$fileName,sep=""),phenoData=a d) > eset <- gcrma(raw,fast=FALSE) trying URL 'http://bioconductor.org/packages/2.2/data/annotation/src/contrib/ mu11ksubacdf_2.2.0.tar.gz' Content type 'application/x-gzip' length 437563 bytes (427 Kb) opened URL ================================================== downloaded 427 Kb * Installing *source* package 'mu11ksubacdf' ... ** R ** data ** help >>> Building/Updating help pages for package 'mu11ksubacdf' Formats: text html latex example geometry text html latex example mu11ksubacdf text html latex mu11ksubadim text html latex ** building package indices ... * DONE (mu11ksubacdf) The downloaded packages are in /tmp/RtmpCmPqvz/downloaded_packages Adjusting for optical effect............Done. Computing affinities[1] "Checking to see if your internet connection works..." trying URL 'http://bioconductor.org/packages/2.2/data/annotation/src/contrib/ mu11ksubaprobe_2.2.0.tar.gz' Content type 'application/x-gzip' length 1191866 bytes (1.1 Mb) opened URL ================================================== downloaded 1.1 Mb * Installing *source* package 'mu11ksubaprobe' ... ** R ** data ** help >>> Building/Updating help pages for package 'mu11ksubaprobe' Formats: text html latex example mu11ksubaprobe text html latex example ** building package indices ... * DONE (mu11ksubaprobe) The downloaded packages are in /tmp/RtmpCmPqvz/downloaded_packages .Done. Adjusting for non-specific binding.Error in pms[, i] <- GSB.adj(Yin = pms[, i], subset = index.affinities, : number of items to replace is not a multiple of replacement length > eset <- gcrma(raw,fast=FALSE) Adjusting for optical effect............Done. Computing affinities.Done. Adjusting for non-specific binding.Error in pms[, i] <- GSB.adj(Yin = pms[, i], subset = index.affinities, : number of items to replace is not a multiple of replacement length > package.version("gcrma") [1] "2.12.1" > traceback() 3: gcrma.engine(pms = pm(object), mms = mm(object), ncs, pm.affinities = pmaffinity.info), mm.affinities = mmaffinity.info), anc, type = type, k = k, stretch = stretch, correction = correction, GSB.adjust = GSB.adjust, rho = rho, verbose = verbose, fast = fast) 2: bg.adjust.gcrma(object, affinity.info = affinity.info, affinity.source = affinity.source, NCprobe = NCprobe, type = type, k = k, stretch = stretch, correction = correction, GSB.adjust = GSB.adjust, rho = rho, optical.correct = optical.correct, verbose = verbose, fast = fast) 1: gcrma(raw, fast = FALSE) >