After adding >comb95 <- res$cdf rma normalization works well when using rma() or expresso(). Sorrowly, mas5 does not work, neither mas5() nor expresso(), in both cases I get the error: >dat.mas <- mas5(res$dat) background correcting...Error in as.vector(data) : NAs in foreign function call (arg 2) In addition: Warning message: NAs introduced by coercion Of course, mas5 can be calculated separately for U95A and U95Av2, but it would be nice, if it could also be used with the combined affybatch. 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 -----Original Message----- From: Stratowa,Dr.,Christian FEX BIG-AT-V Sent: Wednesday, March 08, 2006 15:06 To: 'bioconductor at stat.math.ethz.ch' Subject: Error with CDF environment when using combineAffyBatch of package matchprobes 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