[BioC] GSEABase and Broad Inst Sets

Iain Gallagher iaingallagher at btopenworld.com
Tue Jul 6 13:32:36 CEST 2010


Hi List

I'm trying to carry out a GSEA analysis on an ExpressionSet object using GSEABase and the Broad Institute genesets (well the C2 subset, specifically).

library(GSEABase)

broadSets <- getBroadSets("/home/iain/Desktop/prostateProjectJN_GS/CEL/msigdb_v2.5.xml")# file downloaded from Broad site

isC2 <- sapply(broadSets, function(x) bcCategory(collectionType(x))) == "c2"

broadSetsC2<-broadSets[isC2]

relevantArrays <- grep('Hypo.No.None|Norm.No.None', TS)

relevantArrays <- rmaDataFiltered[ ,relevantArrays]

So this get me to the point where I have my expression data and the genesets I want. This is where I'm having trouble. Following the GSEABase tutorials with KEGG annotation I have no problems; but I can't calculate an incidence matrix from my expression data using the Broad genesets I have downloaded. 

i.e.

testGSC <- GeneSetCollection(relevantArrays, setType=BroadCollection())
Error in get(mapName, envir = pkgEnv, inherits = FALSE) : 
  object 'hgu133plus2BROAD' not found
Error in revmap(getAnnMap(toupper(collectionType(setType)), annotation(idType))) : 
  error in evaluating the argument 'x' in selecting a method for function 'revmap'


This is a mapping issue I know but I'm having a conceptual block getting over it. If anyone could offer any help I'd be grateful.

iain

> sessionInfo()
R version 2.10.1 (2009-12-14) 
x86_64-pc-linux-gnu 

locale:
 [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8    
 [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8   
 [7] LC_PAPER=en_GB.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] affyQCReport_1.24.0  affyPLM_1.22.0       preprocessCore_1.8.0
 [4] xtable_1.5-6         simpleaffy_2.22.0    gcrma_2.18.1        
 [7] latticeExtra_0.6-11  lattice_0.18-3       RColorBrewer_1.0-2  
[10] hgu133plus2.db_2.3.5 hgu133plus2cdf_2.5.0 affy_1.24.2         
[13] limma_3.2.3          GSEABase_1.8.0       graph_1.26.0        
[16] annotate_1.24.1      hgu95av2.db_2.3.5    org.Hs.eg.db_2.3.6  
[19] RSQLite_0.9-0        DBI_0.2-5            AnnotationDbi_1.8.2 
[22] genefilter_1.28.2    ALL_1.4.7            Biobase_2.6.1       

loaded via a namespace (and not attached):
[1] affyio_1.14.0      Biostrings_2.14.12 grid_2.10.1        IRanges_1.4.16    
[5] splines_2.10.1     survival_2.35-8    tools_2.10.1       XML_3.1-0         
> 





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