[BioC] Encountering error when using GOstats package

[Rich Savage]

Hi all,

I'm using the GOstats package to find significant GO terms.  This has been 
working fine but I've just upgraded to the R version 2.7.2 (and the latest 
versions of the Bioconductor packages) and I now get an error.  I've had no luck 
trying to fix this and so am hoping someone an help me!


EXAMPLE CODE:

library(GO.db);
library(GOstats);
library(ath1121501.db);
geneIDs <- c("AT1G21670","AT4G19960","AT5G37600","AT1G56220","AT1G53310")
params  <- new("GOHyperGParams", geneIds=geneIDs, annotation="ath1121501.db",
                 ontology='MF', pvalueCutoff=0.05, conditional=TRUE, 	
                 testDirection = "over");
hgTestResult <- hyperGTest(params);


WHICH PRODUCES AN ERROR WHEN RUNNING THE "hyperGTest" FUNCTION:
Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
   variable "ath1121501ENTREZID" was not found
Error in mget(probes, ID2EntrezID(datPkg)) :
   error in evaluating the argument 'envir' in selecting a method for function 
'mget'


TRACEBACK
14: mget(probes, ID2EntrezID(datPkg))
13: unlist(mget(probes, ID2EntrezID(datPkg)))
12: unique(unlist(mget(probes, ID2EntrezID(datPkg))))
11: getUniverseHelper(probes, datPkg, entrezIds)
10: getUniverseViaGo(p)
9: universeBuilder(p)
8: universeBuilder(p)
7: is(object, Cl)
6: is(object, Cl)
5: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase",
        "hyperGTest")
4: hyperGTest(params)


SESSION INFO
R version 2.7.2 (2008-08-25)
i386-apple-darwin8.11.1

locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets 
methods   base

other attached packages:
  [1] ath1121501_2.2.0    ath1121501cdf_2.2.0 ath1121501.db_2.2.0 GOstats_2.6.0 
       Category_2.6.0      genefilter_1.20.0   survival_2.34-1     RBGL_1.16.0 
        annotate_1.18.0
[10] xtable_1.5-3        graph_1.18.1        GO.db_2.2.0 
AnnotationDbi_1.2.2 RSQLite_0.7-0       DBI_0.2-4           Biobase_2.0.1

loaded via a namespace (and not attached):
[1] cluster_1.11.11



I'd be very grateful for any help you can offer!

Many thanks,

Rich

-- 
------------------------------------------------------------------
   Dr. Richard Savage			Tel: +44 (0)24 765 50243
   Systems Biology Centre		
   University of Warwick
   Coventry
   CV4 7AL
   United Kingdom

   Web:  http://www.programming4scientists.com/
   	http://wsbc.warwick.ac.uk/~richsavage/