Hi John,

Is there any specific reason why your universeGeneIds is an empty character
vector? I think that might have something to do with things not working out
quite as you would think.

tony

On Wed, May 6, 2009 at 8:57 AM, John Coulthard <bahhab@hotmail.com> wrote:

>
> Hi
>
> Could someone please help me out with this error on a hyperGTest with KEGG
> parameters? I get the same error on the hgu133plus2 chip. Must be something
> wrong with my parameter definition but I can't work out what.
>
> > params<-new("KEGGHyperGParams", geneIds =entrez_set0.05,
> universeGeneIds = character(0), annotation = "mouse4302", testDirection
> ="over")
>
> > hgkegg<- hyperGTest(params)
>
> Error in get(paste(lib, name, sep = "")) :
>
>  variable "mouse4302PATH2EG" was not found
>
> More details below.
> Many thanks
> John
>
>
> > class(entrez_set0.05)
> [1] "character"
> > head(entrez_set0.05)
> [1] "2673"  "3977"  "687"   "54510" "51101" "6926"
> > ls("package:mouse4302.db")
>  [1] "mouse4302"              "mouse4302ACCNUM"
>  "mouse4302ALIAS2PROBE"
>  [4] "mouse4302CHR"           "mouse4302CHRLENGTHS"    "mouse4302CHRLOC"
>  [7] "mouse4302CHRLOCEND"     "mouse4302_dbconn"       "mouse4302_dbfile"
> [10] "mouse4302_dbInfo"       "mouse4302_dbschema"     "mouse4302ENSEMBL"
> [13] "mouse4302ENSEMBL2PROBE" "mouse4302ENTREZID"      "mouse4302ENZYME"
> [16] "mouse4302ENZYME2PROBE"  "mouse4302GENENAME"      "mouse4302GO"
> [19] "mouse4302GO2ALLPROBES"  "mouse4302GO2PROBE"      "mouse4302MAP"
> [22] "mouse4302MAPCOUNTS"     "mouse4302MGI"           "mouse4302MGI2PROBE"
> [25] "mouse4302ORGANISM"      "mouse4302PATH"
>  "mouse4302PATH2PROBE"
> [28] "mouse4302PFAM"          "mouse4302PMID"
>  "mouse4302PMID2PROBE"
> [31] "mouse4302PROSITE"       "mouse4302REFSEQ"        "mouse4302SYMBOL"
> [34] "mouse4302UNIGENE"       "mouse4302UNIPROT"
> >  params<-new("KEGGHyperGParams", geneIds =entrez_set0.05, universeGeneIds
> = character(0), annotation = "mouse4302", testDirection ="over")
> > hgkegg<- hyperGTest(params)
> Error in get(paste(lib, name, sep = "")) :
>  variable "mouse4302PATH2EG" was not found
> >
>
>
> > sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-redhat-linux-gnu
>
> locale:
>
> LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_US.utf8;LC_MONETARY=C;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] gtools_2.5.0        GOstats_2.8.0       Category_2.8.3
>  [4] genefilter_1.22.0   survival_2.34-1     RBGL_1.18.0
>  [7] annotate_1.20.1     xtable_1.5-5        GO.db_2.2.5
> [10] graph_1.20.0        RMySQL_0.7-2        KEGG.db_2.2.5
> [13] mouse4302.db_2.2.5  moe430b.db_2.2.5    RSQLite_0.7-1
> [16] DBI_0.2-4           AnnotationDbi_1.4.2 Biobase_2.2.2
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.11 GSEABase_1.4.0  XML_1.98-1
>
>
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