Hello, I tried to do annotation by hgu133plus2 package and got the following error message. Would anyone tell me how to fix it? Thanks a lot! Yanqin > annosam <- aafTableAnn(samNames,"hgu133plus2",aaf.handler()) Error in mget(c("1555832_s_at", "1555847_a_at", "201169_s_at", "201236_s_at", : recursive default argument reference > sessionInfo() R version 2.1.0, 2005-04-18, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: hgu133plus2cdf annaffy GO KEGG hgu133plus2 "1.5.1" "1.0.17" "1.6.5" "1.6.5" "1.8.4" annotate siggenes affy reposTools Biobase "1.5.1-1" "1.2.11" "1.5.8-1" "1.5.2" "1.5.0" --------------------------------- [[alternative HTML version deleted]]

Hello Seth, Thanks for your suggestion! I did update all packages by choosing 'update packages' option in the package menu. I tried to rerun my code and unfortunately something wrong with ReadAffy function. The following is error message. Would you help me out? Really appreciate your help! Yanqin > dat <- ReadAffy(filenames=filenames,phenoData="phenodata.txt",verbose=TRUE) 1 reading DWar-ABO-INK006_Post-1a-U133APlus2.CEL ...instantiating an AffyBatch (intensity a 1354896x10 matrix)...done. Reading in : DWar-ABO-INK006_Post-1a-U133APlus2.CEL ...................................................................... ................ Error in inherits(x, "factor") : Object "mapCdfName" not found In addition: Warning message: data set 'mapCdfName' not found in: data(mapCdfName, envir = environment()) > dat Error: Object "dat" not found > sessionInfo() R version 2.1.0, 2005-04-18, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: affy reposTools Biobase "1.6.7" "1.5.19" "1.5.12" > __________________________________________________ [[alternative HTML version deleted]]