[BioC] hthgu133adim not found

[James W. MacDonald]

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
> 
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-- 
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