[BioC] GSEABase error parsing msigdb_v3.1.xml

[Martin Morgan]

On 01/31/2013 02:37 AM, Lina Hultin-Rosenberg wrote:
> 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!

thank you for the report; this is updated in version 1.20.2, which should be 
available Friday at 10am ish Seattle time.

The only way to import a single category is to use just a subset of the original 
data in its XML representation downloaded from 
http://www.broadinstitute.org/gsea/downloads.jsp, as hinted at on ?getObjects 
help page.

Hope that helps,

Martin

>
>
> 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
>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>


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

Location: Arnold Building M1 B861
Phone: (206) 667-2793