Dear James Thank you, this seems to be indeed the case. What I did was: >comb95cdf <- res$cdf Meanwhile a colleague told me to add: >res$dat at cdfName <- "comb95" and this solved the problem, too. 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: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Wednesday, March 08, 2006 15:51 To: Stratowa,Dr.,Christian FEX BIG-AT-V Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Error with CDF environment when using combineAffyBatch of package matchprobes 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