Hi, I was wondering if anyone might have some ideas as to why I might be having a problem using ReadAffy with the mouse chip moe430acdf. I get the same error whether I use my cel files or cel files downloaded from the web. An example file is a cel file umass_A1D0-430A-1[1].CEL.zip which I downloaded from the web http://www.diabetesgenome.org/cgi-bin/chipperdb/expt.cgi?id=61 , unzipped and put it in same directory from which I was running R. Below I have put the commands, error and traceback for reading the single file from the web. >ReadAffy(file="umass_A1D0-430A-1.CEL") Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : invalid object for as.environment AffyBatch object size of arrays=712x712 features (3965 kb) cdf=MOE430A (??? affyids) number of samples=1 Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : invalid object for as.environment In addition: Warning message: missing cdf environment ! in: show(list()) > traceback() 10: cdfFromEnvironment(cdfname, cur$where, verbose) 9: switch(cur$what, environment = cdfFromEnvironment(cdfname, cur$where, verbose), data = cdfFromData(cdfname, cur$where, verbose), libPath = cdfFromLibPath(cdfname, cur$where, verbose = verbose), bioC = cdfFromBioC(cdfname, cur$where, verbose)) 8: getCdfInfo(object) 7: geneNames(object) 6: geneNames(object) 5: cat("number of genes=", length(geneNames(object)), "\n", sep = "") 4: show(list()) 3: show(list()) 2: print.default(list()) 1: print(list()) > I got the error using R version 2.0.1 and the release version of Affy, reposTools and Biobase (see following sessionInfo) >sessionInfo() R version 2.0.1, 2004-11-15, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: moe430acdf affy reposTools Biobase "1.4.3" "1.5.8-1" "1.5.12" "1.5.5" I then tried again with the latest R version 2.1.0 and the developmental versions of the packages and got the same error. > sessionInfo() R version 2.0.1, 2004-11-15, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: moe430acdf affy reposTools Biobase "1.4.3" "1.6.4" "1.5.15" "1.5.7" My machine is Windows XP Professional Version 2002. I have now uninstalled all my old versions of R in case something was interfering and have reinstalled R version 2.1.0 but I still have the same error. I would really appreciate any advice concerning what may be happening here!!! Regards Marg Dr Margaret Gardiner-Garden Garvan Institute of Medical Research Sydney Australia

Hi Margaret, "Margaret Gardiner-Garden" <m.gardiner-garden@garvan.org.au> writes: > I was wondering if anyone might have some ideas as to why I might be > having a problem using ReadAffy with the mouse chip moe430acdf. Unfortunately, I don't have a solution for you, but we will look into it here and get back to you. I must, however, take a moment to thank you for a well written problem report :-) Best, + seth

Hi Margaret, "Margaret Gardiner-Garden" <m.gardiner-garden@garvan.org.au> writes: > I get the same error whether I use my cel files or cel files downloaded from > the web. An example file is a cel file umass_A1D0-430A-1[1].CEL.zip which I > downloaded from the web > http://www.diabetesgenome.org/cgi-bin/chipperdb/expt.cgi?id=61 , unzipped > and put it in same directory from which I was running R. We weren't able to reproduce there error you've reported. It seems quite likely that the CEL file that you downloaded was corrupted in the download process, the "[1]" on the filename is a hint. I just downloaded the file and get an md5sum as: c7cf96006751fbb4c805548c7d6b8915 umass_A1D0-430A-1.CEL.zip Please give a try at downloading again and rerunning the analysis. + seth