Dear Bioconductor, I have been trying to generate gcrma expression estimates from CEL files, and I obtain the error message shown below. The CEL files were generated from the Arabidopsis ATH1 array. The error message suggests that bioconductor does not have the cdf file for the ATH1 array....is that correct? Thanks very much, William R. Swindell Michigan State University > library(affy) > mydata = ReadAffy() > library(gcrma) > eset = gcrma(mydata) > Computing affinities[1] "Checking to see if your internet connection works..." Warning message: cannot open: HTTP status was '404 Not Found' Note: http://www.bioconductor.org/CRANrepository does not seem to have a valid repository, skipping Warning message: Failed to read replisting at http://www.bioconductor.org/CRANrepository in: getReplisting(repURL, repFile, method = method) Warning message:

William Robert Swindell wrote: > Dear Bioconductor, > I have been trying to generate gcrma expression estimates from CEL files, > and I obtain the error message shown below. The CEL files were generated > from the Arabidopsis ATH1 array. The error message suggests that > bioconductor does not have the cdf file for the ATH1 array....is that > correct? > Thanks very much, > William R. Swindell > Michigan State University > > >>library(affy) >>mydata = ReadAffy() >>library(gcrma) >>eset = gcrma(mydata) >> > > > Computing affinities[1] "Checking to see if your internet connection > works..." > Warning message: > cannot open: HTTP status was '404 Not Found' > Note: http://www.bioconductor.org/CRANrepository does not seem to have a > valid repository, skipping > Warning message: > Failed to read replisting at http://www.bioconductor.org/CRANrepository in: > getReplisting(repURL, repFile, method = method) > Warning message: This doesn't imply that the package is not there - HTTP status was '404 Not Found' means that you couldn't connect to the BioC webserver. Likely possibilities are a.)BioC was down when you tried (it's up now), or b.) MSU uses a proxy server and you need to set your R to use the internet2.dll (assuming you are on Windows - you don't mention your OS). If this is true, see FAQ 2.19 http://cran.fhcrc.org/bin/windows/base/rw-FAQ.html#The-Internet- download-functions-fail_002e HTH, Jim > > _______________________________________________ > 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 University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.