Using a recent version of R, I get an error running gcrma on hthgu133a (high throughput Affymetrix U133A) chips. The error is Error in pms[, i] <- GSB.adj(Yin = pms[, i], subset = index.affinities, : number of items to replace is not a multiple of replacement length Calls: gcrma -> bg.adjust.gcrma -> gcrma.engine Execution halted ___ Here are the details ... [root at cbiodev74 GCRMATEST]# uname -a Linux cbiodev74.xxx.xxx.xxx 2.6.9-67.ELsmp #1 SMP Wed Nov 7 13:56:44 EST 2007 x86_64 x86_64 x86_64 GNU/Linux [root at cbiodev74 GCRMATEST]# cat j2.R library(affy) library(hthgu133acdf) library(hthgu133aprobe) library(gcrma) dat <- ReadAffy(); eset <- gcrma(dat) write.exprs(eset,file="output.gcrma.txt") bye("no") [root at cbiodev74 GCRMATEST]# cat j2.R | R --vanilla R version 2.7.1 (2008-06-23) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 <blah blah="" ...="" boilerplate="" startup="" messages="" removed="" to="" keep="" it="" short=""> Type 'q()' to quit R. > library(affy) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: affyio Loading required package: preprocessCore > library(hthgu133acdf) > library(hthgu133aprobe) Loading required package: matchprobes > library(gcrma) Loading required package: splines > dat <- ReadAffy(); > eset <- gcrma(dat) 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 Calls: gcrma -> bg.adjust.gcrma -> gcrma.engine Execution halted [root at cbiodev74 GCRMATEST]#