Hi, I am getting errors from annaffy when I try to use it on "mgu74av2", depending on what columns I request/exclude or call the function a second time: > anncols <- aaf.handler() #all! > andiff <- aafTableAnn(probeTop, "mgu74av2", anncols ) Error in `parent.env<-`(`*tmp*`, value = NULL) : use of NULL environment is defunct > andiff <- aafTableAnn(probeTop, "mgu74av2", anncols ) Error in exists(num$GOID, GOTERM) : recursive default argument reference In an old post I found this could be because of conflicting package versions. I reinstalled mgu74av2 and annaffy but this did not help. Thank you very much in advance, ido > sessionInfo() R version 2.4.1 (2006-12-18) x86_64-redhat-linux-gnu attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: annaffy KEGG GO mgu74av2 mgu74av2probe "1.6.1" "1.10.0" "1.10.0" "1.14.0" "1.14.0" mgu74av2cdf limma affyQCReport simpleaffy genefilter "1.14.0" "2.9.1" "1.12.0" "2.8.0" "1.12.0" survival plier gcrma matchprobes geneplotter "2.30" "1.4.0" "2.6.0" "1.6.0" "1.12.0" annotate affy affyio Biobase "1.12.1" "1.12.2" "1.0.0" "1.12.2"

Hi Ido, One problem is that your GO and KEGG packages are absolutely ancient. The current versions are 1.14.1, so you need to update those. I use annaffy all the time, and I don't see these errors, so try updating GO and KEGG and see if that fixes things. Best, Jim Ido M. Tamir wrote: > Hi, > > I am getting errors from annaffy when I try to use it > on "mgu74av2", depending on what columns I request/exclude > or call the function a second time: > > >> anncols <- aaf.handler() #all! >> andiff <- aafTableAnn(probeTop, "mgu74av2", anncols ) > > Error in `parent.env<-`(`*tmp*`, value = NULL) : > use of NULL environment is defunct > >> andiff <- aafTableAnn(probeTop, "mgu74av2", anncols ) > > Error in exists(num$GOID, GOTERM) : recursive default argument reference > > In an old post I found this could be because of conflicting package versions. > I reinstalled mgu74av2 and annaffy but this did not help. > > Thank you very much in advance, > ido > > > >>sessionInfo() > > R version 2.4.1 (2006-12-18) > x86_64-redhat-linux-gnu > > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "methods" "base" > > other attached packages: > annaffy KEGG GO mgu74av2 mgu74av2probe > "1.6.1" "1.10.0" "1.10.0" "1.14.0" "1.14.0" > mgu74av2cdf limma affyQCReport simpleaffy genefilter > "1.14.0" "2.9.1" "1.12.0" "2.8.0" "1.12.0" > survival plier gcrma matchprobes geneplotter > "2.30" "1.4.0" "2.6.0" "1.6.0" "1.12.0" > annotate affy affyio Biobase > "1.12.1" "1.12.2" "1.0.0" "1.12.2" > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.