[BioC] KEGGHyperGParams variable "mouse4302PATH2EG" was not found

[Marc Carlson]

Hi John,

At least part of your trouble is caused by an old bug that does not
exist in modern versions of Bioconductor.  Your problem should clear up
if you simply update the Category package, but for best results I would
encourage you to install the newest 2.9 release of R and the more recent
2.4 release of Bioconductor.

At a bare minimum you should do this:

source("http://bioconductor.org/biocLite.R")
biocLite("Category")


Which should at least update Category to version 2.8.4. 

Please let us know if you have any more questions.


  Marc




John Coulthard 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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