Hi, I have been trying to use gcrma to get expression indexes from mouse 430_2 affymetrix arrays. However, I cannot get the appropriate CDF file if I run 'just.gcrma'. Below is the error message. It seems that the downloading URL is incorrect - but how should I fix this? Thanks very much, Yi Xing 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: cannot open: HTTP status was '404 Not Found' Note: http://www.bioconductor.org/packages/bioc/devel does not seem to have a valid repository, skipping Warning messages: 1: Failed to read replisting at http://www.bioconductor.org/packages/bioc/devel in: getReplisting(repURL, repFile, method = method) 2: cannot open: HTTP status was '404 Not Found' Note: http://www.bioconductor.org/packages/data/annotation/stable does not seem to have a valid repository, skipping Warning messages: 1: Failed to read replisting at http://www.bioconductor.org/packages/data/annotation/stable in: getReplisting(repURL, repFile, method = method) 2: cannot open: HTTP status was '404 Not Found' Note: http://www.bioconductor.org/packages/data/annotation/devel does not seem to have a valid repository, skipping Warning messages: 1: Failed to read replisting at http://www.bioconductor.org/packages/data/annotation/devel in: getReplisting(repURL, repFile, method = method) 2: cannot open: HTTP status was '404 Not Found' Note: http://www.bioconductor.org/packages/data/experiment/stable does not seem to have a valid repository, skipping Warning messages: 1: Failed to read replisting at http://www.bioconductor.org/packages/data/experiment/stable in: getReplisting(repURL, repFile, method = method) 2: cannot open: HTTP status was '404 Not Found' Note: http://www.bioconductor.org/packages/data/annotation/stable does not seem to have a valid repository, skipping Warning messages: 1: Failed to read replisting at http://www.bioconductor.org/packages/data/annotation/stable in: getReplisting(repURL, repFile, method = method) 2: cannot open: HTTP status was '404 Not Found' Note: http://www.bioconductor.org/packages/data/annotation/stable does not seem to have a valid repository, skipping Warning messages: 1: Failed to read replisting at http://www.bioconductor.org/packages/data/annotation/stable in: getReplisting(repURL, repFile, method = method) 2: cannot open: HTTP status was '404 Not Found' Note: http://www.bioconductor.org/packages/omegahat/stable does not seem to have a valid repository, skipping Warning messages: 1: Failed to read replisting at http://www.bioconductor.org/packages/omegahat/stable in: getReplisting(repURL, repFile, method = method) 2: cannot open: HTTP status was '404 Not Found' Note: http://www.bioconductor.org/packages/lindsey/stable does not seem to have a valid repository, skipping Note: Using download type: Source Error in getCDF(cdfpackagename) : Environment mouse4302cdf was not found in the Bioconductor repository. In addition: Warning message: Failed to read replisting at http://www.bioconductor.org/packages/lindsey/stable in: getReplisting(repURL, repFile, method = method)

Yi Xing wrote: > Hi, > > I have been trying to use gcrma to get expression indexes from mouse > 430_2 affymetrix arrays. However, I cannot get the appropriate CDF file > if I run 'just.gcrma'. Below is the error message. It seems that the > downloading URL is incorrect - but how should I fix this? You don't give your sessionInfo(), so it is hard to say exactly what the problem is. In addition, this doesn't look like the output you should get if justGCRMA() can't load the correct URL. It looks more like you were trying to install packages using an outdated reposTools package (which is defunct in BioC 1.9, and superceded by biocLite()). At the very least it appears you need to update Biobase to get a current biocReposList(), so I would start with source("http://www.bioconductor.org/biocLite.R") biocLite("Biobase") While you are at it, you can just get the mouse4302cdf and probe packages as well. biocLite(c("mouse4302cdf", "mouse4302probe")) Best, Jim > > Thanks very much, > Yi Xing > > 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: > cannot open: HTTP status was '404 Not Found' > Note: http://www.bioconductor.org/packages/bioc/devel does not seem to > have a valid repository, skipping > Warning messages: > 1: Failed to read replisting at > http://www.bioconductor.org/packages/bioc/devel in: > getReplisting(repURL, repFile, method = method) > 2: cannot open: HTTP status was '404 Not Found' > Note: http://www.bioconductor.org/packages/data/annotation/stable does > not seem to have a valid repository, skipping > Warning messages: > 1: Failed to read replisting at > http://www.bioconductor.org/packages/data/annotation/stable in: > getReplisting(repURL, repFile, method = method) > 2: cannot open: HTTP status was '404 Not Found' > Note: http://www.bioconductor.org/packages/data/annotation/devel does > not seem to have a valid repository, skipping > Warning messages: > 1: Failed to read replisting at > http://www.bioconductor.org/packages/data/annotation/devel in: > getReplisting(repURL, repFile, method = method) > 2: cannot open: HTTP status was '404 Not Found' > Note: http://www.bioconductor.org/packages/data/experiment/stable does > not seem to have a valid repository, skipping > Warning messages: > 1: Failed to read replisting at > http://www.bioconductor.org/packages/data/experiment/stable in: > getReplisting(repURL, repFile, method = method) > 2: cannot open: HTTP status was '404 Not Found' > Note: http://www.bioconductor.org/packages/data/annotation/stable does > not seem to have a valid repository, skipping > Warning messages: > 1: Failed to read replisting at > http://www.bioconductor.org/packages/data/annotation/stable in: > getReplisting(repURL, repFile, method = method) > 2: cannot open: HTTP status was '404 Not Found' > Note: http://www.bioconductor.org/packages/data/annotation/stable does > not seem to have a valid repository, skipping > Warning messages: > 1: Failed to read replisting at > http://www.bioconductor.org/packages/data/annotation/stable in: > getReplisting(repURL, repFile, method = method) > 2: cannot open: HTTP status was '404 Not Found' > Note: http://www.bioconductor.org/packages/omegahat/stable does not > seem to have a valid repository, skipping > Warning messages: > 1: Failed to read replisting at > http://www.bioconductor.org/packages/omegahat/stable in: > getReplisting(repURL, repFile, method = method) > 2: cannot open: HTTP status was '404 Not Found' > Note: http://www.bioconductor.org/packages/lindsey/stable does not seem > to have a valid repository, skipping > Note: Using download type: Source > Error in getCDF(cdfpackagename) : Environment mouse4302cdf was not > found in the Bioconductor repository. > In addition: Warning message: > Failed to read replisting at > http://www.bioconductor.org/packages/lindsey/stable in: > getReplisting(repURL, repFile, method = method) > > _______________________________________________ > 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC 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.