[BioC] GSVA questions

[Joe [guest]]

Dear Markus,
 
I do it as you said, “c2BroadSets”source from package, and "C5allBraodSets" is load from GMT file that download from broadinstitute.
as: 
> c2BroadSets
GeneSetCollection
  names: NAKAMURA_CANCER_MICROENVIRONMENT_UP, NAKAMURA_CANCER_MICROENVIRONMENT_DN, ..., ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY (3272 total)
  unique identifiers: 5167, 100288400, ..., 57191 (29340 total)
  types in collection:
    geneIdType: EntrezIdentifier (1 total)
    collectionType: BroadCollection (1 total)
 
> C5allBroadSets
GeneSetCollection
  names: NUCLEOPLASM, EXTRINSIC_TO_PLASMA_MEMBRANE, ..., INOSITOL_OR_PHOSPHATIDYLINOSITOL_KINASE_ACTIVITY (1454 total)
  unique identifiers: HNRPK, XRCC6, ..., PGM1 (8299 total)
  types in collection:
    geneIdType: NullIdentifier (1 total)
    collectionType: NullCollection (1 total)
 
when I use "c2BroadSets" GeneSetCollection,  it works, and "NSCLC_norm_GSE32474_rma_Filter" is ExpressionSet, Because of customized CDF, unique gene ID used in the file, so I adjust the min.sz to 1
>NSCLC_gsva_c2 <- gsva(NSCLC_norm_GSE32474_rma_Filter, c2BroadSets,min.sz=1, max.sz=500, verbose=TRUE)$es.obs
 
when I use "C5allBroadSets", report error, as
>NSCLC_gsva_c5 <- gsva(NSCLC_norm_GSE32474_rma_Filter, C5allBroadSets,min.sz=1, max.sz=500, verbose=TRUE)$es.obs
Mapping identifiers between gene sets and feature names
Error in GSVA:::.gsva(Biobase::exprs(expr), mapped.gset.idx.list, method,  : 
  The gene set list is empty!  Filter may be too stringent.
 
SO, how could I set parameters and make gsva work.................
 
Thanks,
Joe

 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936   
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C                                                   
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936    

attached base packages:
 [1] splines   grid      parallel  stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] GSVA_1.8.0                       GSVAdata_0.99.10                
 [3] hgu95a.db_2.9.0                  hgu133plus2hsentrezgprobe_17.1.0
 [5] hgu133plus2hsentrezgcdf_17.1.0   hgu133plus2hsentrezg.db_17.1.0  
 [7] hgu95av2.db_2.9.0                a4Classif_1.8.0                 
 [9] varSelRF_0.7-3                   randomForest_4.6-7              
[11] pamr_1.54.1                      survival_2.37-4                 
[13] ROCR_1.0-5                       gplots_2.11.3                   
[15] KernSmooth_2.23-10               caTools_1.14                    
[17] gdata_2.13.2                     gtools_3.0.0                    
[19] MLInterfaces_1.40.0              sfsmisc_1.0-24                  
[21] cluster_1.14.4                   rda_1.0.2-2                     
[23] rpart_4.1-3                      MASS_7.3-29                     
[25] a4Preproc_1.8.0                  a4Core_1.8.0                    
[27] glmnet_1.9-5                     Matrix_1.0-12                   
[29] lattice_0.20-23                  GSEABase_1.22.0                 
[31] affy_1.38.1                      GOstats_2.26.0                  
[33] graph_1.38.3                     Category_2.26.0                 
[35] VennDiagram_1.6.5                pheatmap_0.7.6                  
[37] statmod_1.4.17                   limma_3.16.7                    
[39] biomaRt_2.16.0                   annotate_1.38.0                 
[41] genefilter_1.42.0                primeviewhsentrezgprobe_17.1.0  
[43] primeviewhsentrezg.db_17.1.0     org.Hs.eg.db_2.9.0              
[45] RSQLite_0.11.4                   DBI_0.2-7                       
[47] primeviewhsentrezgcdf_17.1.0     AnnotationDbi_1.22.6            
[49] Biobase_2.20.1                   BiocGenerics_0.6.0              
[51] rj_1.1.3-1                      

loaded via a namespace (and not attached):
 [1] affyio_1.28.0         AnnotationForge_1.2.2 BiocInstaller_1.10.3 
 [4] bitops_1.0-6          GO.db_2.9.0           IRanges_1.18.3       
 [7] mboost_2.2-2          preprocessCore_1.22.0 RBGL_1.36.2          
[10] RCurl_1.95-4.1        rj.gd_1.1.3-1         stats4_3.0.1         
[13] tools_3.0.1           XML_3.98-1.1          xtable_1.7-1         
[16] zlibbioc_1.6.0 

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