[BioC] hthgu133adim not found

Richard Finney rfinney5 at yahoo.com
Mon Jun 23 23:20:24 CEST 2008


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



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