[BioC] Trouble using GOstats

[Robert Gentleman]

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)
>>
>
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> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
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| Robert Gentleman              phone: (206) 667-7700                    
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| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
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| Fred Hutchinson Cancer Research Center                                 
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| email: rgentlem at fhcrc.org                                              
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