[BioC] gcrma problem under Debian

[Ting-Yuan Liu (FHCRC)]

Hi, 

Could you give us more information about the version of gcrma you used?  
You can use sessionInfo() to get the information.  Moreover, if the 12 
arrays are available online, could you also provide the link for us to 
download the arrays and test it?

I try to run 4 hgu133a arrays in gcrma, and there is no error occured.  
Here is what I did:

####################################################################

> library(gcrma)
Loading required package: affy
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor 
	 Vignettes contain introductory material.  To view, 
	 simply type: openVignette() 
	 For details on reading vignettes, see
	 the openVignette help page.
Loading required package: reposTools
Loading required package: matchprobes
> data <- ReadAffy()
> eset <- gcrma(data)
> data 
AffyBatch object
size of arrays=712x712 features (15851 kb)
cdf=HG-U133A (22283 affyids)
number of samples=4
number of genes=22283
annotation=hgu133a
> eset
Expression Set (exprSet) with 
	22283 genes
	4 samples
		 phenoData object with 1 variables and 4 cases
	 varLabels
		sample: arbitrary numbering
> sessionInfo()
R version 2.1.0, 2005-04-20, x86_64-unknown-linux-gnu 

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  
"grDevices"
[7] "utils"     "datasets"  "base"     

other attached packages:
hgu133aprobe   hgu133acdf        gcrma  matchprobes         affy   
reposTools 
       "1.0"      "1.4.3"      "1.1.3"     "1.0.12"    "1.5.8-1"      
"1.5.2" 
     Biobase 
     "1.5.0" 

####################################################################

HTH, 

Ting-Yuan

On Fri, 29 Apr 2005, Stefano Calza wrote:

> Hi.
> 
> I'm having problem with R and gcrma, i.e. using gcrma (12 arrays, hgu133a) R keep exiting with segmentation fault.
> 
> Any hint?
> 
> Info:
> 
> Debian
> platform i386-pc-linux-gnu
> arch     i386             
> os       linux-gnu        
> system   i386, linux-gnu  
> status                    
> major    2                
> minor    1.0              
> year     2005             
> month    04               
> day      18               
> language R
> 
> Bioconductor devel
> 
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