I used rgu34a version 1.7.0 package for my annotation last week and it worked very well. However, when I tried to use the same code to run my new gene list for annotation this morning, I kept getting the error message. I went to bioconductor and redownload the rgu34a package although I believed it didn't change within last few days. And I still got the same error message. Would anyone tell me where I could find the correct version of rgu34a package for R2.1.0? atab <- aafTableAnn( Names, "rgu34a", aaf.handler() ) [1] "You have package rgu34a but the incorrect version" Note: http://www.bioconductor.org/data/metaData does not seem to have a valid repository, skipping Warning message: Failed to read replisting at http://www.bioconductor.org/data/metaData in: getReplisting(repURL, repFile, method = method) Note: http://www.bioconductor.org/data/metaData-devel does not seem to have a valid repository, skipping Error in hasFiles(rep) : no direct or inherited method for function 'hasFiles' for this call In addition: Warning message: Failed to read replisting at http://www.bioconductor.org/data /metaData-devel in: getReplisting(repURL, repFile, method = method) Thanks a lot! Yanqin --------------------------------- [[alternative HTML version deleted]]

Hi Jim, Thanks for the suggestion. I tried it and it didn't work out. I got the same error message as before. Any other suggestion I could try? Thanks! Yanqin James MacDonald <jmacdon@med.umich.edu> wrote: Hi Yanquin, This is due to a slight bug in annaffy. The quick fix is to open the DESCRIPTION file in the rgu34a package directory with an editor and change the version field to say 1.6.8 . It should then work. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Yanqin Yang 5/12/2005 12:34:49 PM >>> I used rgu34a version 1.7.0 package for my annotation last week and it worked very well. However, when I tried to use the same code to run my new gene list for annotation this morning, I kept getting the error message. I went to bioconductor and redownload the rgu34a package although I believed it didn't change within last few days. And I still got the same error message. Would anyone tell me where I could find the correct version of rgu34a package for R2.1.0? atab <- aafTableAnn( Names, "rgu34a", aaf.handler() ) [1] "You have package rgu34a but the incorrect version" Note: http://www.bioconductor.org/data/metaData does not seem to have a valid repository, skipping Warning message: Failed to read replisting at http://www.bioconductor.org/data/metaData in: getReplisting(repURL, repFile, method = method) Note: http://www.bioconductor.org/data/metaData-devel does not seem to have a valid repository, skipping Error in hasFiles(rep) : no direct or inherited method for function 'hasFiles' for this call In addition: Warning message: Failed to read replisting at http://www.bioconductor.org/data/metaData-devel in: getReplisting(repURL, repFile, method = method) Thanks a lot! Yanqin --------------------------------- [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. --------------------------------- [[alternative HTML version deleted]]

Hi Jim, It worked! Thank you very much! Actually, it turned out R download the rgu34a 1.7.0 again since I changed the version number in the DESCRIPTION file. Did I use the wrong version of annaffy package? Thanks again! Yanqin James MacDonald <jmacdon@med.umich.edu> wrote: Try this version of annaffy. Let me know if it works (I am assuming you are on windows). Jim >>> Yanqin Yang 5/12/2005 2:37:55 PM >>> Hi Jim, Thanks for the suggestion. I tried it and it didn't work out. I got the same error message as before. Any other suggestion I could try? Thanks! Yanqin James MacDonald wrote: Hi Yanquin, This is due to a slight bug in annaffy. The quick fix is to open the DESCRIPTION file in the rgu34a package directory with an editor and change the version field to say 1.6.8 . It should then work. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Yanqin Yang 5/12/2005 12:34:49 PM >>> I used rgu34a version 1.7.0 package for my annotation last week and it worked very well. However, when I tried to use the same code to run my new gene list for annotation this morning, I kept getting the error message. I went to bioconductor and redownload the rgu34a package although I believed it didn't change within last few days. And I still got the same error message. Would anyone tell me where I could find the correct version of rgu34a package for R2.1.0? atab <- aafTableAnn( Names, "rgu34a", aaf.handler() ) [1] "You have package rgu34a but the incorrect version" Note: http://www.bioconductor.org/data/metaData does not seem to have a valid repository, skipping Warning message: Failed to read replisting at http://www.bioconductor.org/data/metaData in: getReplisting(repURL, repFile, method = method) Note: http://www.bioconductor.org/data/metaData-devel does not seem to have a valid repository, skipping Error in hasFiles(rep) : no direct or inherited method for function 'hasFiles' for this call In addition: Warning message: Failed to read replisting at http://www.bioconductor.org/data/metaData-devel in: getReplisting(repURL, repFile, method = method) Thanks a lot! Yanqin --------------------------------- [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. --------------------------------- ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. __________________________________________________ [[alternative HTML version deleted]]