Dear List, I have been trying to find GO category enrichment in one of my gene lists. The list is derived from hgu133a. When I run the function "GOHyperG", I get an error which is shown below. If I use the default lib="hgu95av", there is no error. I am at a loss. Please help.... Thanks Ramsi > library(hgu133a) > list.of.genes <- read.table(file = "top185.txt") > sig.genes <- list.of.genes[, 1] > uni.sig.genes <- unique(sig.genes) > go.analysis <- GOHyperG(uni.sig.genes, lib = "hgu133a", what = "BP") Error in FUN(X[[15]], ...) : No direct or inherited method for function "Ontology" for this call > > traceback() 9: FUN(X[[15]], ...) 8: lapply(as.list(X), FUN, ...) 7: sapply(wh, Ontology) 6: getGOOntology(names(goV)) 5: unlist(getGOOntology(names(goV))) 4: GOHyperG(uni.sig.genes, lib = "hgu133a", what = "BP") 3: eval.with.vis(expr, envir, enclos) 2: eval.with.vis(ei, envir) 1: source("gostats.R", echo = T) >

On Mar 31, 2005, at 1:19 PM, Ramsi Haddad wrote: > Dear List, > > I have been trying to find GO category enrichment in one of my gene > lists. The list is derived from hgu133a. When I run the function > "GOHyperG", I get an error which is shown below. If I use the default > lib="hgu95av", there is no error. I am at a loss. Please help.... > > Thanks > > Ramsi > >> library(hgu133a) > >> list.of.genes <- read.table(file = "top185.txt") > >> sig.genes <- list.of.genes[, 1] > >> uni.sig.genes <- unique(sig.genes) > >> go.analysis <- GOHyperG(uni.sig.genes, lib = "hgu133a", > what = "BP") > Error in FUN(X[[15]], ...) : No direct or inherited method for function > "Ontology" for this call >> >> traceback() > 9: FUN(X[[15]], ...) > 8: lapply(as.list(X), FUN, ...) > 7: sapply(wh, Ontology) > 6: getGOOntology(names(goV)) > 5: unlist(getGOOntology(names(goV))) > 4: GOHyperG(uni.sig.genes, lib = "hgu133a", what = "BP") > 3: eval.with.vis(expr, envir, enclos) > 2: eval.with.vis(ei, envir) > 1: source("gostats.R", echo = T) > Ramsi, I think this has come up before on the list and has to do with differing versions of GOstats, GO, and your annotation package. Make sure you are up-to-date on all fronts. Sean

Hi Ramsi, First you really need to tell us a bit more about your installation, what packages etc. Using sessionInfo gives a reasonably complete list. Telling us, "they are up to date" is not informative. Version numbers are essential. Second, it is considered good style to also give a completely runnable example so that anyone willing to help can run it and see if they get the error. Perhaps using only a small set of your sig.genes For example I just something with: R version 2.1.0, 2005-03-25, powerpc-apple-darwin7.7.0 attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: Rgraphviz hgu133a hgu95av2 GOstats multtest reposTools genefilter "1.5.7" "1.7.0" "1.7.0" "1.1.2" "1.5.4" "1.5.14" "1.5.3" survival xtable RBGL annotate GO XML graph "2.16" "1.2-5" "1.3.8" "1.5.10" "1.7.0" "0.95-6" "1.5.4" Biobase Ruuid cluster "1.5.7" "1.5.0" "1.9.7" Without any errors. Are you sure that your gene list is LocusLink identifiers? Best wishes, Robert On Mar 31, 2005, at 10:19 AM, Ramsi Haddad wrote: > Dear List, > > I have been trying to find GO category enrichment in one of my gene > lists. The list is derived from hgu133a. When I run the function > "GOHyperG", I get an error which is shown below. If I use the default > lib="hgu95av", there is no error. I am at a loss. Please help.... > > Thanks > > Ramsi > >> library(hgu133a) > >> list.of.genes <- read.table(file = "top185.txt") > >> sig.genes <- list.of.genes[, 1] > >> uni.sig.genes <- unique(sig.genes) > >> go.analysis <- GOHyperG(uni.sig.genes, lib = "hgu133a", > what = "BP") > Error in FUN(X[[15]], ...) : No direct or inherited method for function > "Ontology" for this call >> >> traceback() > 9: FUN(X[[15]], ...) > 8: lapply(as.list(X), FUN, ...) > 7: sapply(wh, Ontology) > 6: getGOOntology(names(goV)) > 5: unlist(getGOOntology(names(goV))) > 4: GOHyperG(uni.sig.genes, lib = "hgu133a", what = "BP") > 3: eval.with.vis(expr, envir, enclos) > 2: eval.with.vis(ei, envir) > 1: source("gostats.R", echo = T) >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+