[BioC] Trouble using GOstats

[Sean Davis]

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