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

[Martin Morgan]

Hi Alice --

"Johnstone, Alice" <Alice.Johnstone at esr.cri.nz> writes:

> 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'

Bug, unfortunately, should be fixed in GSEABase_1.2.2 available noon
tomorrow PST.

Sorry about that,

Martin

> 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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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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Phone: (206) 667-2793