OK. I have R 2.1 installed. Have "all" of bioconductor installed. Most everything works as expected, excepting that when I try to use affylmGUI, it works (including the GCRMA support, which is great), until the point where the probes are matched to the annotations. At that point I get a string of error messages including: Error in mget(ls(cdfenv),env = mgu74av2GENENAME) : Object "mgu74av2GENENAME" not found It downloads the annotation files on its own, and does so successfully. What is causing this? Thanks, Anand C. Patel, MD Fellow, Pediatric Pulmonology St. Louis Children's Hospital acpatel@usa.net

Anand C.Patel wrote: > OK. I have R 2.1 installed. Have "all" of bioconductor installed. Most > everything works as expected, excepting that when I try to use affylmGUI, it > works (including the GCRMA support, which is great), until the point where the > probes are matched to the annotations. At that point I get a string of error > messages including: > > Error in mget(ls(cdfenv),env = mgu74av2GENENAME) : > Object "mgu74av2GENENAME" not found > > It downloads the annotation files on its own, and does so successfully. > > What is causing this? It's due to a change in how the annotation packages are being built that hasn't been completely resolved as yet. A simple solution is to paste the following code in your R session after you have attached the mgu74av2 annotation package. files <- scan(file.path(.path.package("mgu74av2"),"data","filelist"), what="character") files <- as.list(sub("\\.rda$", "", files[-1])) myEnv <- as.environment("package:mgu74av2") data(list = files, envir = myEnv) Then you should be able to proceed as normal. HTH, Jim > > Thanks, > Anand C. Patel, MD > Fellow, Pediatric Pulmonology > St. Louis Children's Hospital > acpatel@usa.net > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109