When running gcrma on htghu133a chips, I get this error message: Computing affinities.Error in get(x, envir, mode, inherits) : variable "hthgu133adim" was not found Execution halted Anybody got any idea what's wrong? I'm running Linux/R2.5 Gory details here ... uname -a Linux lxxxxxxx.xxx.xxx.gov 2.6.9-67.0.7.ELsmp #1 SMP Wed Feb 27 04:47:23 EST 2008 x86_64 x86_64 x86_64 GNU/Linux -bash-3.00$ 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") -bash-3.00$ cat j2.R | R --vanilla R version 2.5.0 (2007-04-23) <blah blah="" ...="" boilerplate="" removed=""> > 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 > 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.Error in get(x, envir, mode, inherits) : variable "hthgu133adim" was not found Execution halted

Hi Richard, Richard Finney wrote: > When running gcrma on htghu133a chips, I get this > error message: > Computing affinities.Error in get(x, envir, mode, > inherits) : variable "hthgu133adim" was not found > Execution halted > > Anybody got any idea what's wrong? > > I'm running Linux/R2.5 The first step is to upgrade to a less ancient version of R and BioC. Without a sessionInfo(), I can't be sure, but I would bet you have some mis-matched versions in there. Best, Jim > Gory details here ... > > uname -a > Linux lxxxxxxx.xxx.xxx.gov 2.6.9-67.0.7.ELsmp #1 SMP > Wed Feb 27 04:47:23 EST 2008 x86_64 x86_64 x86_64 > GNU/Linux > -bash-3.00$ 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") > -bash-3.00$ cat j2.R | R --vanilla > > R version 2.5.0 (2007-04-23) > <blah blah="" ...="" boilerplate="" removed=""> > >> 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 >> 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.Error in get(x, envir, mode, > inherits) : variable "hthgu133adim" was not found > Execution halted > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623