Dear Christoph, What not do the data preprocessing step in Expression Consol software, then export the data with annotations as a text file, then import into R for further analysis. To import data into R, you can use read.delim or read.csv functions. Best regards, Anthony -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Christoph Knapp Sent: Sunday, April 18, 2010 3:36 PM To: bioconductor@stat.math.ethz.ch Subject: [BioC] hugene10stv1cdf Hi all, I'm trying for quite some time to get an analysis started. I keep getting this Error. Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuGene-1_0-st-v1 Library - package hugene10stv1cdf not installed Bioconductor - hugene10stv1cdf not available Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo Execution halted I installed all possible packages from there http://www.bioconductor.org/docs/workflows/oligoarrays/ and even downloaded and installed that one http://mbi00206.bio.med.uni-muenchen.de/free/pd.hugene.1.0.st.v1.zip) still no change. What am I missing? It reads in the CEL files VFdata=ReadAffy() but when I look at the VFdata object it already says > VFdata AffyBatch object size of arrays=1050x1050 features (11 kb) cdf=HuGene-1_0-st-v1 (??? affyids) number of samples=7 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuGene-1_0-st-v1 Library - package hugene10stv1cdf not installed Bioconductor - hugene10stv1cdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch) and going on > eset = exprs(rma(VFdata)) Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuGene-1_0-st-v1 Library - package hugene10stv1cdf not installed Bioconductor - hugene10stv1cdf not available Error in exprs(rma(VFdata)) : error in evaluating the argument 'object' in selecting a method for function 'exprs' > I'm very inexperienced in terms of stuff like that. A answer for dummies would be much appreciated. Thanks Christoph _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- believed to be clean. ###################################################################### ############### This e-mail message has been scanned for Viruses and Content and cleared by MailMarshal ###################################################################### ############### ###################################################################### ############### This e-mail message has been scanned for Viruses and Content and cleared by MailMarshal ###################################################################### ############### [[alternative HTML version deleted]]