Hi,

GSVA probably needs the geneIdType slot:

>> c2BroadSets

>    geneIdType: EntrezIdentifier (1 total)

Below you are using HGNC symbols, so you need to set geneIdType to SymbolIdentifier.

>> 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)

Hope that will work.

Markus

> 
> 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 
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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