Hi Yanqin, Yanqin Yang <yanqin_yang@yahoo.com> writes: > error message. Would anyone tell me how to fix it? > > 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" You seem to have quite a mix of old and new Bioconductor packages and I would wager that this is the source of your troubles. Try upgrading (reinstalling) the Bioconductor packages so that you are current with the latest release, Bioc 1.6. In particular, you'll need to upgrade: annaffy, GO, KEGG, annotate, siggenes, affy, reposTools, Biobase. Then give it another shot and report back if you encounter the same (or different) difficulties. + seth