GSVA questions
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I'm a GSVA package new user. One question make me confused. If I used custom CDF (download from BrainArray website), usually, the custom CDF file has unique ProbeID correspond to one gene, so this format expression data could be used in GSVA? Another one, exclude c2BroadSet, is there any GeneSellection data could be used or download? -- 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] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] genefilter_1.42.0 primeviewhsentrezgprobe_17.1.0 [3] primeviewhsentrezg.db_17.1.0 org.Hs.eg.db_2.9.0 [5] RSQLite_0.11.4 DBI_0.2-7 [7] primeviewhsentrezgcdf_17.1.0 AnnotationDbi_1.22.6 [9] Biobase_2.20.1 BiocGenerics_0.6.0 [11] rj_1.1.3-1 loaded via a namespace (and not attached): [1] annotate_1.38.0 IRanges_1.18.3 rj.gd_1.1.3-1 splines_3.0.1 [5] stats4_3.0.1 survival_2.37-4 tools_3.0.1 XML_3.98-1.1 [9] xtable_1.7-1 -- Sent via the guest posting facility at bioconductor.org.
cdf GSVA cdf GSVA • 1.5k views
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Dan Tenenbaum ★ 8.2k
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CC'ing GSVA maintainer. On Thu, Sep 5, 2013 at 5:45 PM, Joe [guest] <guest at="" bioconductor.org=""> wrote: > > I'm a GSVA package new user. One question make me confused. If I used custom CDF (download from BrainArray website), usually, the custom CDF file has unique ProbeID correspond to one gene, so this format expression data could be used in GSVA? > Another one, exclude c2BroadSet, is there any GeneSellection data could be used or download? > > -- 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] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] genefilter_1.42.0 primeviewhsentrezgprobe_17.1.0 > [3] primeviewhsentrezg.db_17.1.0 org.Hs.eg.db_2.9.0 > [5] RSQLite_0.11.4 DBI_0.2-7 > [7] primeviewhsentrezgcdf_17.1.0 AnnotationDbi_1.22.6 > [9] Biobase_2.20.1 BiocGenerics_0.6.0 > [11] rj_1.1.3-1 > > loaded via a namespace (and not attached): > [1] annotate_1.38.0 IRanges_1.18.3 rj.gd_1.1.3-1 splines_3.0.1 > [5] stats4_3.0.1 survival_2.37-4 tools_3.0.1 XML_3.98-1.1 > [9] xtable_1.7-1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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
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Hi Joe, BrainArray provides annotation packages (*.db_version.tar.gz) for all custom CDFs and looks like you installed the correct one. According to the GSVA documentation, following code should work with GSVAdata: gsva(eset, c2BroadSet, ...) (probably requiring that annotation(eset) returns "primeviewhsentrezg") or gsva(matrix, c2BroadSet, annotation="primeviewhsentrezg" ,...) Alternatively, use these annotation packages to convert (i) your genesets to probeset ids or (ii) the probeset ids to the gene identifiers used in your genesets. For the latter: symbols <- lookUp(featureNames(eset), annotation(eset), "SYMBOL") featureNames(eset) <- symbols Here the links to some useful gene sets in the GMT file format (there are lots of parsers in Bioconductor and CRAN, most simple to use is probably GSA::GSA.read.gmt. To get a similar gene set object as c2BroadSet, use the GSEABase package): http://www.broadinstitute.org/gsea/msigdb/index.jsp http://compbio.dfci.harvard.edu/genesigdb/downloadall.jsp Cheers, Markus On Sep 5, 2013, at 8:48 PM, Dan Tenenbaum wrote: > CC'ing GSVA maintainer. > > On Thu, Sep 5, 2013 at 5:45 PM, Joe [guest] <guest@bioconductor.org> wrote: >> >> I'm a GSVA package new user. One question make me confused. If I used custom CDF (download from BrainArray website), usually, the custom CDF file has unique ProbeID correspond to one gene, so this format expression data could be used in GSVA? >> Another one, exclude c2BroadSet, is there any GeneSellection data could be used or download? >> >> -- 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] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] genefilter_1.42.0 primeviewhsentrezgprobe_17.1.0 >> [3] primeviewhsentrezg.db_17.1.0 org.Hs.eg.db_2.9.0 >> [5] RSQLite_0.11.4 DBI_0.2-7 >> [7] primeviewhsentrezgcdf_17.1.0 AnnotationDbi_1.22.6 >> [9] Biobase_2.20.1 BiocGenerics_0.6.0 >> [11] rj_1.1.3-1 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.38.0 IRanges_1.18.3 rj.gd_1.1.3-1 splines_3.0.1 >> [5] stats4_3.0.1 survival_2.37-4 tools_3.0.1 XML_3.98-1.1 >> [9] xtable_1.7-1 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- DFCI Biostatistics & Computational Biology Office Location: Center for Life Science Building, Room 11052 Phone: +1-617-582-7586 [[alternative HTML version deleted]]
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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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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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- DFCI Biostatistics & Computational Biology Office Location: Center for Life Science Building, Room 11052 Phone: +1-617-582-7586 [[alternative HTML version deleted]]
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Dear Joe, the function gsva() needs to match the identifiers from the ExpressionSet object with those from the gene sets. This is done using the available Bioconductor infrastructure for this purpose which relies on gene-centric annotation packages typically anchored at Entrez Gene Identifiers. Notice that the object 'c2BroadSets' has its gene set definitions in terms of Entrez identifiers and this facilitates the matching operation with ExpressionSet objects. In principle, this should not be a problem if you download the .gmt files from the Broad that contain the gene set definitions in terms of Entrez Gene identifiers. cheers, robert. On 09/06/2013 07:46 AM, Joe [guest] wrote: > > 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. > > _______________________________________________ > 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 > -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 fax: +34.933.160.550
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