GSEABase error in parsing msigdb_v2.5.xml

Hi,

I get error reading the last vesrsion of Broad msigdb . Is it supposed
to work?

> gss <- getBroadSets('/data/PathDB/msigdb_v2.5.xml')
Error: 'getBroadSets' failed to create gene sets:
  invalid BroadCollection category: 'c5'
> traceback()
6: stop("'getBroadSets' failed to create gene sets:\n  ",
conditionMessage(err), 
       call. = FALSE)
5: value[[3]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       geneSets <- unlist(mapply(.fromXML, uri, "//GENESET", factories, 
           SIMPLIFY = FALSE, USE.NAMES = FALSE))
   }, error = function(err) {
       stop("'getBroadSets' failed to create gene sets:\n  ",
conditionMessage(err), 
           call. = FALSE)
   })
1: getBroadSets("/data/PathDB/msigdb_v2.5.xml")
> packageDescription('GSEABase')
Package: GSEABase
Type: Package
Title: Gene set enrichment data structures and methods
Version: 1.2.0
Author: Martin Morgan, Seth Falcon, Robert Gentleman
Maintainer: Biocore Team c/o BioC user list
        <bioconductor@...>
Description: This package provides classes and methods to support Gene
        Set Enrichment Analysis (GSEA).
License: Artistic-2.0
Depends: R (>= 2.6.0), methods, AnnotationDbi, Biobase, annotate
Suggests: Ruuid, hgu95av2.db, GO.db, org.Hs.eg.db
Imports: methods, XML, graph
LazyLoad: yes
biocViews: Infrastructure, Statistics
Collate: utilities.R AAA.R AllClasses.R AllGenerics.R getObjects.R
        methods-CollectionType.R methods-ExpressionSet.R
        methods-GeneColorSet.R methods-GeneIdentifierType.R
        methods-GeneSet.R methods-GeneSetCollection.R
        methods-OBOCollection.R zzz.R
Packaged: Wed Apr 30 02:43:40 2008; biocbuild
Built: R 2.7.0; ; 2008-05-14 16:18:51; unix

-- File: /usr/local/lib64/R/library/GSEABase/Meta/package.rds 

 
Althogh
getBroadSets('/data/PathDB/msigdb_v2.1.xml')
works. I don's see obvios signs of corruption in the 2.5.xml
[rstats:GeneLogic070523] head -n 2 /data/PathDB/*.xml
==> /data/PathDB/msigdb_v2.1.xml <==
<?xml version="1.0" encoding="UTF-8"?>

==> /data/PathDB/msigdb_v2.5.xml <==
<?xml version="1.0" encoding="UTF-8"?>

tail -n 2 /data/PathDB/*.xml
==> /data/PathDB/msigdb_v2.1.xml <==
  <GENESET STANDARD_NAME="GNF2_ZAP70" SYSTEMATIC_NAME="c4:526"
ORGANISM="Human" CHIP="GENE_SYMBOL" CATEGORY_CODE="c4"
CONTRIBUTOR="Broad Institute" CONTRIBUTOR_ORG="Broad Institute"
DESCRIPTION_BRIEF="Neighborhood of ZAP70" DESCRIPTION_FULL="Neighborhood
of ZAP70 zeta-chain (TCR) associated protein kinase 70kDa  in the GNF2
expression compendium" TAGS=""
MEMBERS="ZAP70,PTPN4,UNC84B,TUSC4,CTSW,RARRES3,BTN3A2,NKG7,PRKCH,KLRK1,B
TN3A3,MYBL1,GZMA,ARL4C,SH2D1A,TXK,CD7,RORA,CD247,IL18RAP,CD96,RASGRP1,GZ
MM,TRD@,MATK,ITGAL,KLRB1"
MEMBERS_SYMBOLIZED="ZAP70,PTPN4,UNC84B,TUSC4,CTSW,RARRES3,BTN3A2,NKG7,PR
KCH,KLRK1,BTN3A3,MYBL1,GZMA,ARL4C,SH2D1A,TXK,CD7,RORA,CD247,IL18RAP,CD96
,RASGRP1,GZMM,TRD@,MATK,ITGAL,KLRB1"/>
</MSIGDB>

==> /data/PathDB/msigdb_v2.5.xml <==
  <GENESET
STANDARD_NAME="INOSITOL_OR_PHOSPHATIDYLINOSITOL_KINASE_ACTIVITY"
SYSTEMATIC_NAME="c5:1203" ORGANISM="Homo sapiens" AUTHORS="Ashburner M,
Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski
K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A,
Lewis S, Matese JC,Richardson JE, Ringwald M, Rubin GM, Sherlock G."
EXTERNAL_DETAILS_URL="http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
?view=details&amp;search_constraint=terms&amp;depth=0&amp;query=GO:00044
28" CHIP="GENE_SYMBOL" CATEGORY_CODE="c5" CONTRIBUTOR="Gene Ontology"
CONTRIBUTOR_ORG="Gene Ontology" DESCRIPTION_BRIEF="Genes annotated by
the GO term GO:0004428. Catalysis of the phosphorylation of myo-inositol
(1,2,3,5/4,6-cyclohexanehexol) or a phosphatidylinositol."
DESCRIPTION_FULL="" TAGS="Molecular function"
MEMBERS="FXN,SMG1,PIP4K2B,PIP5K3,ATM,PIK3C2A,PIK3C3,PIK3CA,PIK3CB,PIK3CG
,PIK3R2,PIK3R3,IPPK,PI4KA,PI4KB,PI4K2A,ITPKA,ITPKB"
MEMBERS_SYMBOLIZED="FXN,SMG1,PIP4K2B,PIP5K3,ATM,PIK3C2A,PIK3C3,PIK3CA,PI
K3CB,PIK3CG,PIK3R2,PIK3R3,IPPK,PI4KA,PI4KB,PI4K2A,ITPKA,ITPKB"/>
</MSIGDB>

 

Best
Vlad

Vladimir Morozov 

ALS Therapy Development Institute 

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