Hi, all, I'm at Cornell university. I'm trying to use the affy package to analyze canine 2.0 arrays, I can read in CEL files into "myAffyBatch", but running show(myAffyBatch) give error below, could someone help (human arrays work fine for me)? Thanks a lot. Wei "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 `403 Forbidden' Note: http://www.bioconductor.org/repository/devel/package/Source does not seem to have a valid repository, skipping Warning messages: 1: Failed to read replisting at http://www.bioconductor.org/repository/devel/package/Source in: getReplisting(repURL, repFile, method = method) 2: cannot open: HTTP status was `403 Forbidden' Note: http://www.bioconductor.org/repository/devel/package/Win32 does not seem to have a valid repository, skipping Note: You did not specify a download type. Using a default value of: Win32 This will be fine for almost all users Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment specified did not contain Canine_2 Library - package canine2cdf not installed Data for package affy did not contain Canine_2 Bioconductor - canine2cdf not available In addition: Warning message: Failed to read replisting at http://www.bioconductor.org/repository/devel/package/Win32 in: getReplisting(repURL, repFile, method = method) "

Hi Wei, You seem to be having problems connecting to the repository. Does source("http://www.bioconductor.org/biocLite.R") biocLite("canine2cdf") work for you? You should also always give your sessionInfo(). It may be that you have a very old R version for which there isn't a canine2cdf (in which case you should upgrade to R-2.5.1 at the very least). Best, Jim Wei Wang wrote: > Hi, all, > > I'm at Cornell university. I'm trying to use the affy package to analyze > canine 2.0 arrays, I can read in CEL files into "myAffyBatch", but running > show(myAffyBatch) give error below, could someone help (human arrays work > fine for me)? Thanks a lot. > > Wei > > "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 `403 Forbidden' > Note: http://www.bioconductor.org/repository/devel/package/Source does not > seem to have a valid repository, skipping > Warning messages: > 1: Failed to read replisting at > http://www.bioconductor.org/repository/devel/package/Source in: > getReplisting(repURL, repFile, method = method) > 2: cannot open: HTTP status was `403 Forbidden' > Note: http://www.bioconductor.org/repository/devel/package/Win32 does not > seem to have a valid repository, skipping > Note: You did not specify a download type. Using a default value of: Win32 > This will be fine for almost all users > > Error in getCdfInfo(object) : Could not obtain CDF environment, problems > encountered: > Specified environment specified did not contain Canine_2 > Library - package canine2cdf not installed > Data for package affy did not contain Canine_2 > Bioconductor - canine2cdf not available > In addition: Warning message: > Failed to read replisting at > http://www.bioconductor.org/repository/devel/package/Win32 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