[BioC] KEGGHyperGParams variable "mouse4302PATH2EG" was not found

[Marc Carlson]

Related to Tonys observation, you might find the GOstats vignette on
Hypergeometric testing to be a helpful resource:

http://www.bioconductor.org/packages/2.4/bioc/html/GOstats.html


  Marc



Tony Chiang wrote:
> 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 at 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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