[BioC] Trouble using GOstats

[Ramsi Haddad]

Dear Sean,
  Thanks for the reply.  All my packages are from the most recent
version of bioC and R.  This problem occurs on two computers that I have
it installed on.  Both are linux (one is my desktop, the other is a
remote machine).   I guess on both machines, R is not installed but is
run from the directory from which it resides.  I installed all the
packages using R CMD INSTALL.
Ramsi


On Thu, 2005-03-31 at 16:19, Sean Davis wrote:
> 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
>