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? Best regards Christian ============================================== Christian Stratowa, PhD Boehringer Ingelheim Austria Dept NCE Lead Discovery - Bioinformatics Dr. Boehringergasse 5-11 A-1121 Vienna, Austria Tel.: ++43-1-80105-2470 Fax: ++43-1-80105-2782 email: christian.stratowa at vie.boehringer-ingelheim.com

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$dat) I think you missed a step here. You have to point to the cdfenv to use. From the vignette: comb <- res$cdf <-- This puts the correct cdfenv into your .GlobalEnv so rma() can find it. z <- rma(res$dat) So I think you need to add comb95 <- res$cdf before your call to rma(). HTH, Jim -- 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

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? 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