[BioC] Trouble using GOstats
Robert Gentleman
rgentlem at fhcrc.org
Thu Mar 31 23:46:11 CEST 2005
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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| Head, Program in Computational Biology fax: (206) 667-1319 |
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