[BioC] GSEA GeneSetCollection for GO info from Illumina annotation package

[Johnstone, Alice]

Hi,
I am having some trouble creating a geneset collection for GO data from
the Illumina annotation package illuminaRatBCv1.  I can create the KEGG
set fine as shown below, but when I try the same for GO info I get the
error below:

>
illumina.rat.kegg<-GeneSetCollection(idType=AnnotationIdentifier("illumi
naRatBCv1"),setType=KEGGCollection())
> illumina.rat.kegg
GeneSetCollection
  names: 04110, 00400, ..., 00640 (184 total)
  unique identifiers: 2260270, 5900358, ..., 580441 (2557 total)
  types in collection:
    geneIdType: AnnotationIdentifier (1 total)
    collectionType: KEGGCollection (1 total)


>
illumina.rat.go<-GeneSetCollection(idType=AnnotationIdentifier("illumina
RatBCv1"),setType=GOCollection())
Error in as.vector(x, "character") : 
  cannot coerce type 'S4' to vector of type 'character'
Error in as.list(getAnnMap("GO2PROBE", idType)) : 
  error in evaluating the argument 'x' in selecting a method for
function 'as.list'


Could someone help me out with whats going wrong?
Thank you!
Alice



> sessionInfo()
R version 2.7.0 (2008-04-22) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New
Zealand.1252;LC_MONETARY=English_New
Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252

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

[8] base     

other attached packages:
 [1] GO.db_2.2.0           GSEABase_1.2.1        illuminaRatBCv1_1.1.0
 [4] beadarray_1.8.0       affy_1.18.0           preprocessCore_1.2.0 
 [7] affyio_1.8.0          geneplotter_1.18.0    annotate_1.18.0      
[10] xtable_1.5-2          AnnotationDbi_1.2.0   RSQLite_0.6-8        
[13] DBI_0.2-4             lattice_0.17-6        Biobase_2.0.1        
[16] limma_2.14.1         

loaded via a namespace (and not attached):
[1] cluster_1.11.10    graph_1.18.0       grid_2.7.0
KernSmooth_2.22-22
[5] RColorBrewer_1.0-2 XML_1.93-2.1  




Alice Johnstone

PhD Student
Institute of Environmental Science and Research Ltd
Kenepuru Science Centre
34 Kenepuru Drive
PO Box 50-348
Porirua
New Zealand

Tel:  + 64 4 914-0717
Fax: + 64 4 914-0770


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