[BioC] Error with CDF environment when using combineAffyBatch of package matchprobes

[Wolfgang Huber]

Hi Christian

please see the vignette: you'll need to put the contents of
res$cdf into the global workspace, so that rma can find it:

comb95 <- res$cdf.

Best wishes
  Wolfgang


-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber
-------------------------------------


Christian.Stratowa at vie.boehringer-ingelheim.com wrote:
> Hi, 
> 
> I would like to combine U95A and U95Av2 files for RMA, and tried to use
> function 
> combineAffyBatch of package matchprobes (version 1.2.1) as described in the
> vignette: 
> 
>>library(matchprobes) 
>>library(affy) 
>>library(hgu95acdf) 
>>library(hgu95aprobe) 
>>library(hgu95av2cdf) 
> 
> 
> Attaching package: 'hgu95av2cdf' 
> 
> 
>         The following object(s) are masked from package:hgu95acdf : 
> 
>          i2xy xy2i 
> 
> 
>>library(hgu95av2probe) 
> 
> 
>>x95A <- ReadAffy(celfile.path="HG-U95A") 
>>x95Av2 <- ReadAffy(celfile.path="HG-U95Av2") 
>>res <- combineAffyBatch(list(x95A,x95Av2),
> 
> c("hgu95aprobe","hgu95av2probe"), newcdf="comb95") 
> package:hgu95aprobe     hgu95aprobe 
> package:hgu95av2probe   hgu95av2probe 
> 197193 unique probes in common 
> 
> Here is what Iget when doing RMA: 
> 
>>dat.rma <- rma(res$dat) 
> 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/bioc/1.7/src/contrib>
> http://bioconductor.org/packages/bioc/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/data/annotation/1.7/src/contrib>
> http://bioconductor.org/packages/data/annotation/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/data/experiment/1.7/src/contrib>
> http://bioconductor.org/packages/data/experiment/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/omegahat/1.7/src/contrib>
> http://bioconductor.org/packages/omegahat/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/lindsey/1.7/src/contrib>
> http://bioconductor.org/packages/lindsey/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://cran.fhcrc.org/src/contrib> http://cran.fhcrc.org/src/contrib 
> Error in getCdfInfo(object) : Could not obtain CDF environment, problems
> encountered: 
> Specified environment does not contain comb95 
> Library - package comb95cdf not installed 
> Data for package affy did not contain comb95cdf 
> Bioconductor - comb95cdf not available 
> 
> Here is what I get for "res": 
> 
>>res 
> 
> $dat 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/bioc/1.7/src/contrib>
> http://bioconductor.org/packages/bioc/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/data/annotation/1.7/src/contrib>
> http://bioconductor.org/packages/data/annotation/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/data/experiment/1.7/src/contrib>
> http://bioconductor.org/packages/data/experiment/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/omegahat/1.7/src/contrib>
> http://bioconductor.org/packages/omegahat/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/lindsey/1.7/src/contrib>
> http://bioconductor.org/packages/lindsey/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://cran.fhcrc.org/src/contrib> http://cran.fhcrc.org/src/contrib 
> Error in getCdfInfo(object) : Could not obtain CDF environment, problems
> encountered: 
> Specified environment does not contain comb95 
> Library - package comb95cdf not installed 
> Data for package affy did not contain comb95cdf 
> Bioconductor - comb95cdf not available 
> AffyBatch object 
> size of arrays=0x0 features (12328 kb) 
> cdf=comb95 (??? affyids) 
> number of samples=4 
> Warning message: 
> missing cdf environment ! in: show(list()) 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/bioc/1.7/src/contrib>
> http://bioconductor.org/packages/bioc/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/data/annotation/1.7/src/contrib>
> http://bioconductor.org/packages/data/annotation/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/data/experiment/1.7/src/contrib>
> http://bioconductor.org/packages/data/experiment/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/omegahat/1.7/src/contrib>
> http://bioconductor.org/packages/omegahat/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://bioconductor.org/packages/lindsey/1.7/src/contrib>
> http://bioconductor.org/packages/lindsey/1.7/src/contrib 
> Warning: unable to access index for repository
> <http://cran.fhcrc.org/src/contrib> http://cran.fhcrc.org/src/contrib 
> Error in getCdfInfo(object) : Could not obtain CDF environment, problems
> encountered: 
> Specified environment does not contain comb95 
> Library - package comb95cdf not installed 
> Data for package affy did not contain comb95cdf 
> Bioconductor - comb95cdf not available 
> 
> It seems that the newly created CDF environment is not recognized. 
> Does anyone know what might be the reason and how to solve this problem? 
>