All: I am getting an error message with GoHyperG (and a similar error with HyperGTable). library("hgu95av2") w1 <- as.list(hgu95avLOCUSID) w2 <- unique(unlist(w1)) set.seed(123) myLL1 <- sample(w2,100) myLL2 <- c(myLL1, sample(w2,100)) xx <- GOHyperG(myLL1,"hgu95av2",what="BP",universe=myLL2) Error: value for 'GO:0031997' not found > sessionInfo() Version 2.3.0 (2006-04-24) i686-redhat-linux-gnu attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: drosophila2cdf drosophila2 GOstats Category hgu95av2 "1.4.7" "1.12.0" "1.6.0" "1.4.1" "1.12.0" KEGG multtest genefilter survival xtable "1.8.1" "1.10.2" "1.10.1" "2.24" "1.3-2" RBGL annotate Biobase GO graph "1.8.1" "1.10.0" "1.10.1" "1.8.2" "1.10.6" Ruuid "1.10.0" Thanks!! Tony -- ########################### Tony Long Ecology and Evolutionary Biology Steinhaus Hall University of California at Irvine Irvine, CA 92697-2525 Tel: (949) 824-2562 (office) Tel: (949) 824-5994 (lab) Fax: (949) 824-2181 email: tdlong at uci.edu http://hjmuller.bio.uci.edu/~labhome/

Hi Tony, Thanks for including your sessionInfo output. Tony Long <tdlong at="" uci.edu=""> writes: > xx <- GOHyperG(myLL1,"hgu95av2",what="BP",universe=myLL2) > > Error: value for 'GO:0031997' not found I think this is caused by a mismatch between your version of hgu95av2 and GO. Please try the following to update your packages: library("Biobase") update.packages(repos=biocReposList()) Basically, your GO package is too old. + seth

Hi Tony, I think this is caused by a version mismatch on your annotation packages. Generally, you want all of them to be made at the same time so that they're based on the same sources. Your hgu95av2 annotations are version 1.12.0 while GO is at version 1.8.2. It is very likely that hgu95av2 says a probeset is annotated by a GO term which your GO annotation knows nothing about, hence the error. They're separated because the chip annotations only knows about the GO identifier, while the GO annotation can tell you about its name, description and position in the hierarchy. It wouldn't make sense to cause all chip annotations to remember identical information about GO terms. I would suggest updating your annotation packages to the same version and trying again. Francois On Thu, 2006-08-17 at 11:28 -0700, Tony Long wrote: > All: > > I am getting an error message with GoHyperG (and a similar error with > HyperGTable). > > library("hgu95av2") > w1 <- as.list(hgu95avLOCUSID) > w2 <- unique(unlist(w1)) > set.seed(123) > myLL1 <- sample(w2,100) > myLL2 <- c(myLL1, sample(w2,100)) > xx <- GOHyperG(myLL1,"hgu95av2",what="BP",universe=myLL2) > > Error: value for 'GO:0031997' not found > > > sessionInfo() > Version 2.3.0 (2006-04-24) > i686-redhat-linux-gnu > > attached base packages: > [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" > [7] "utils" "datasets" "base" > > other attached packages: > drosophila2cdf drosophila2 GOstats Category hgu95av2 > "1.4.7" "1.12.0" "1.6.0" "1.4.1" "1.12.0" > KEGG multtest genefilter survival xtable > "1.8.1" "1.10.2" "1.10.1" "2.24" "1.3-2" > RBGL annotate Biobase GO graph > "1.8.1" "1.10.0" "1.10.1" "1.8.2" "1.10.6" > Ruuid > "1.10.0" > > Thanks!! > > Tony