[BioC] GSEABase - mapIdentifiers

Martin Morgan mtmorgan at fhcrc.org
Thu Mar 27 01:33:50 CET 2008


Thank you very much for the bug report and reproducible example. This 
has been fixed in the development version of GSEABase, and will appear 
through biocLite after Friday at noon, Seattle time.

An important caveat to using the development version is that the 
representation of GeneIdentifierTypes (e.g., SymbolIdentifier) have been 
changed, so that serialized (e.g., saved) instances of GeneSets and 
GeneColorSets might need to be updated. The update mechanism has not yet 
been thoroughly tested, so if you have saved gene sets that are not 
easily recreated you might wish to hold off on updating GSEABase.

The reason for this change is partly motivated by GOCollections (which 
now know about ontology) and by the desire to map between, e.g., 
SymbolIdentifier and GenenameIdentifier without having to go through 
AnnotationIdentifier. The new mapping allows, for the gene set below

geneIdType(gs) <- GenenameIdentifier("hgu95av2")

(the 'hgu95av2' is new; previously this was only allowed in 
AnnotationIdentifier) which says to use the maps in the hgu95av2 
annotation package to figure out how to get from Symbol to Genename.

Thanks again for the report.


Hans-Ulrich Klein wrote:
> Hello all,
> the function mapIdentifiers() works fine for "GeneSet" objects whereas 
> it throws an error message when a "GeneColorSet" is given:
>  > library("GSEABase")
>  > gs = GeneColorSet(geneIds=c("TYMP", "XPO1", "LBR"),
>                 geneIdType=SymbolIdentifier(),
>                 setName="testlist",
>                 shortDescription="blabla",
>                 phenotype="pheno data",
>                 geneColor = factor(c("increase","increase","increase")),
>                 phenotypeColor = factor(c("A","B","A")))
>  > gs2  = mapIdentifiers(gs, AnnotationIdentifier("hgu95av2"))
> Error in validObject(.Object) :
>   invalid class "GeneColorSet" object: gene and color lengths differ
> It seems that there is a problem when the number of genes/probes in the 
> set changes.
> Regards,
> Hans-Ulrich
>  > sessionInfo()
> R version 2.6.2 (2008-02-08)
> x86_64-pc-linux-gnu
> locale:
> C
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods 
> [8] base    
> other attached packages:
> [1] hgu95av2_2.0.1      Ruuid_1.16.1        GSEABase_1.0.3    
> [4] AnnotationDbi_1.0.6 RSQLite_0.6-8       DBI_0.2-4         
> [7] Biobase_1.16.3    
> loaded via a namespace (and not attached):
> [1] XML_1.93-2      rcompgen_0.1-17
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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

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