[BioC] GSEABase error parsing msigdb_v3.1.xml

[Lina Hultin-Rosenberg]

Dear list,

I am getting an error when trying to parse the latest msigdb version from Broad. I suspect the problem is due to that Broad added another category (c6). Will the new category be included in GSEABase? Is there a way to parse only categories c1-c5, or an alternative way to get all categories? 

See the R code and versions below.

Thank you!


Best regards,

Lina Hultin Rosenberg
PhD student 
Karolinska Institutet
Stockholm, Sweden

#############################################################################
 > library(GSEABase)
> msigdb.file = system.file("extdata", "msigdb_v3.1.xml", package="GSEABase")
> broad.genesets = GeneSet(BroadCollection(), urls=msigdb.file)
Error: 'getBroadSets' failed to create gene sets:
  invalid BroadCollection category: 'c6'
> packageDescription("GSEABase")
Package: GSEABase
Type: Package
Title: Gene set enrichment data structures and methods
Version: 1.20.1
Author: Martin Morgan, Seth Falcon, Robert Gentleman
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
Description: This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).
License: Artistic-2.0
Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), annotate, methods, graph
Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz
Imports: BiocGenerics, annotate, AnnotationDbi, Biobase, graph, methods, XML
LazyLoad: yes
biocViews: Infrastructure, Bioinformatics
Collate: utilities.R AAA.R AllClasses.R AllGenerics.R getObjects.R methods-CollectionType.R methods-ExpressionSet.R methods-GeneColorSet.R methods-GeneIdentifierType.R .....
Packaged: 2012-11-25 06:15:25 UTC; biocbuild
Built: R 2.15.2; ; 2012-11-25 12:32:24 UTC; windows

-- File: C:/Program Files/R/R-2.15.2/library/GSEABase/Meta/package.rds 
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