[BioC] GOstats and org.EcK12.eg.db

[Robert Gentleman]

Hi Robert,
   Yet another one that I will need to write some specialized code for. 
  I should get it done by the end of the week, and will push it to both 
release and devel.  I will post an email when it is done,

  best wishes
    Robert


Robert Castelo wrote:
> dear list,
> 
> I cannot get to work GOstats with the annotation for E. coli in
> org.EcK12.eg.db. Please find below the code that reproduces the problem
> including the error message, and my sessionInfo() at the end of this
> email. I have included the same exercise with the human annotation
> package org.Hs.eg.db which runs fine in my system. Any help with this
> will be very much appreciated.
> 
> thanks!!
> robert.
> ==========CODE STARTS HERE===========
> 
> library(org.Hs.eg.db)
> library(org.EcK12.eg.db)
> library(GOstats)
> 
> geneuniverse <- mappedkeys(org.EcK12.egSYMBOL)
> set.seed(12345)
> geneset <- sample(geneuniverse, size=100, replace=FALSE)
> 
> 
> goHypGparams <- new("GOHyperGParams",
>                     geneIds=geneset,
>                     universeGeneIds=geneuniverse,
>                     annotation="org.EcK12.eg.db", ontology="BP",
>                     pvalueCutoff=1.0, conditional=TRUE,
>                     testDirection="over")
> 
> goHypGcond <- hyperGTest(goHypGparams)
> 
> Error in get(mapName, envir = pkgEnv, inherits = FALSE) : 
>   variable "org.EcK12.egENTREZID" was not found
> Error in mget(probes, ID2EntrezID(datPkg)) : 
>   error in evaluating the argument 'envir' in selecting a method for
> function 'mget'
> 
> geneuniverse <- mappedkeys(org.Hs.egSYMBOL)
> set.seed(12345)
> geneset <- sample(geneuniverse, size=100, replace=FALSE)
> 
> 
> goHypGparams <- new("GOHyperGParams",
>                     geneIds=geneset,
>                     universeGeneIds=geneuniverse,
>                     annotation="org.Hs.eg.db", ontology="BP",
>                     pvalueCutoff=1.0, conditional=TRUE,
>                     testDirection="over")
> 
> goHypGcond <- hyperGTest(goHypGparams)
> 
> 
> sessionInfo()
> R version 2.8.0 beta (2008-10-05 r46601) 
> x86_64-unknown-linux-gnu 
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils
> datasets 
> [8] methods   base     
> 
> other attached packages:
>  [1] org.Hs.eg.db_2.2.6    GOstats_2.7.0         Category_2.7.6       
>  [4] genefilter_1.21.5     survival_2.34-1       RBGL_1.17.2          
>  [7] annotate_1.19.2       xtable_1.5-4          GO.db_2.2.5          
> [10] graph_1.19.6          org.EcK12.eg.db_2.2.6 AnnotationDbi_1.3.12 
> [13] RSQLite_0.7-0         DBI_0.2-4             Biobase_2.1.7        
> 
> loaded via a namespace (and not attached):
> [1] cluster_1.11.11 GSEABase_1.3.6  XML_1.98-1
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org