[BioC] ArrayExpress: missing cdf environment!

[Daniel Rico Rodriguez]

Dear list,

I downloaded a dataset from ArrayExpress using ArrayExpress package,  
and I get an error when I try to see the object created, or a try to  
normalize it with rma.

I am using a Linux Ubuntu. For some reason, a package installation is  
tried (related with cdf, I guess) but I am not root... Is there a way  
to overcome this problem installing some cdf package in my home R  
library folder? I tried installing hgu133a.db, gahgu133acdf and  
u133x3pcdf, and repeating the operation, but I still get the error.

Any help will be really appreciated!

Best,
Daniel

 > library("ArrayExpress")
 > library(affy)
 > GNF <- ArrayExpress("E-TABM-145")
...
  The object containing experiment  E-TABM-145  has been built.
 > class(GNF)
[1] "AffyBatch"
attr(,"package")
[1] "affy"
 > GNF
Warning in install.packages(cdfname, lib = lib, repos =  
Biobase:::biocReposList(),  :
   'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable
AffyBatch object
size of arrays=712x712 features (228 kb)
cdf=HG-U133A (??? affyids)
number of samples=158
Warning in install.packages(cdfname, lib = lib, repos =  
Biobase:::biocReposList(),  :
   'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable
Error in install.packages(cdfname, lib = lib, repos =  
Biobase:::biocReposList(),  :
   unable to install packages
In addition: Warning message:
missing cdf environment! in show(AffyBatch)
 > GNFnorm <- rma(GNF)
Warning in install.packages(cdfname, lib = lib, repos =  
Biobase:::biocReposList(),  :
   'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable
Error in install.packages(cdfname, lib = lib, repos =  
Biobase:::biocReposList(),  :
   unable to install packages

 > sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] affy_1.26.0        ArrayExpress_1.8.0 Biobase_2.8.0

loaded via a namespace (and not attached):
[1] XML_2.8-1             affyio_1.16.0         limma_3.4.0
[4] preprocessCore_1.10.0 tools_2.11.0

********************************************

Daniel Rico Rodriguez, PhD.
Structural Computational Biology Group
Spanish National Cancer Research Center, CNIO
Melchor Fernandez Almagro, 3.
28029 Madrid, Spain.
Phone: +34 91 224 69 00 #3015
drico at cnio.es
http://www.cnio.es

********************************************






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