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

[Robert Castelo]

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