Hello, I meet a problem when I doing rma in microarray analysis. The chip name is Rhesus<http: www.affymetrix.com="" support="" technical="" byproduct.affx?prod="" uct="rhesus"> from Macaca_mulatta by Affymetrix. My R commands are as follow: library(tools) library(limma) library(Biobase) library(affy) targets <- readTargets("affy_targets.txt") data <- ReadAffy(filenames=targets$FileName) eset <- rma(data) There is ana error when I doing RMA. > eset <- rma(data) Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain Rhesus Library - package rhesuscdf not installed Bioconductor - could not connect I also try to install custom CDF file, but failed. Could you help me? Thank you very much in advance. Best, Dong Shan > eset <- justGCRMA() Computing affinities Error in getCDF(cdfpackagename) : The current operation could not access the Bioconductor repository. Please check your internet connection, and report further problems to bioconductor@stat.math.ethz.ch [[alternative HTML version deleted]]

Dear Dong the error message that you get suggests that you verify your internet connection - have you done that, and to what result? The rhesuscdf package is here: http://www.bioconductor.org/packages/release/data/annotation/html/rhes uscdf.html What version of R/Bioconductor are you using? (Have a look at the posting guide, which asks you to provide the output of sessionInfo().) Also, with statements such as "I also try to install custom CDF file, but failed." - try to be more precise. What exactly did you do (report it in a way that others can reproduce it), and what exactly happened to make you think "it" failed (e.g.: copy/paste the error message) Best wishes Wolfgang Il Dec/26/10 7:56 AM, Shan Dong ha scritto: > Hello, > > I meet a problem when I doing rma in microarray analysis. The chip name is > Rhesus<http: www.affymetrix.com="" support="" technical="" byproduct.affx?pr="" oduct="rhesus"> > from > Macaca_mulatta by Affymetrix. > My R commands are as follow: > library(tools) > library(limma) > library(Biobase) > library(affy) > targets<- readTargets("affy_targets.txt") > data<- ReadAffy(filenames=targets$FileName) > eset<- rma(data) > > There is ana error when I doing RMA. >> eset<- rma(data) > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain Rhesus > Library - package rhesuscdf not installed > Bioconductor - could not connect > > > I also try to install custom CDF file, but failed. > Could you help me? > > Thank you very much in advance. > > Best, > > Dong Shan > > >> eset<- justGCRMA() > Computing affinities > Error in getCDF(cdfpackagename) : > The current operation could not access the Bioconductor repository. Please > check your internet connection, and report further problems to > bioconductor at stat.math.ethz.ch > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber