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

Hi Christoph, Christoph Knapp wrote: > Hi all, > I'm trying for quite some time to get an analysis started. I keep > getting this Error. And I gave you the answer you need when you asked this on R-help last week (as did Martin Morgan) https://stat.ethz.ch/pipermail/r-help/2010-April/235479.html yet you continue to ask the same question. Did you try following the advice we gave you? If so, what were the results? If not, why not? Best, Jim > > 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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues