getGmt error
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When I write GMT file into R,like > C2allBroadSets <- getGmt("c2.all.v4.0.orig.gmt") Error in GeneSetCollection(lapply(lines, function(line) { : error in evaluating the argument 'object' in selecting a method for function 'GeneSetCollection': Error in validObject(.Object) : invalid class "GeneSet" object: gene symbols must be unique how to fix it out? -- 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.
GO hgu95a hgu95av2 GO hgu95a hgu95av2 • 2.0k views
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@martin-morgan-1513
Last seen 6 days ago
United States
On 09/05/2013 10:52 PM, Maintainer wrote: > > When I write GMT file into R,like >> C2allBroadSets <- getGmt("c2.all.v4.0.orig.gmt") > Error in GeneSetCollection(lapply(lines, function(line) { : > error in evaluating the argument 'object' in selecting a method for function 'GeneSetCollection': Error in validObject(.Object) : > invalid class "GeneSet" object: gene symbols must be unique the problem is that c2.all.v4.0.orig.gmt (from http://www.broadinstitute.org/gsea/msigdb/collections.jsp) is poorly formed. I did (the output is edited) > options(error=recover) > xx = getGmt("c2.all.v4.0.orig.gmt") Enter a frame number, or 0 to exit 1: getGmt("c2.all.v4.0.orig.gmt") 2: GeneSetCollection(lapply(lines, function(line) { GeneSet(unlist(line[-(1 3: lapply(lines, function(line) { GeneSet(unlist(line[-(1:2)]), geneIdType 4: FUN(X[[4694]], ...) 5: GeneSet(unlist(line[-(1:2)]), geneIdType = geneIdType, collectionType = col 6: GeneSet(unlist(line[-(1:2)]), geneIdType = geneIdType, collectionType = col 7: do.call(new, c("GeneSet", list(geneIds = type), list(... = ..., setIdentifi 8: (function (Class, ...) { ClassDef <- getClass(Class, where = topenv(pare 9: initialize(value, ...) 10: initialize(value, ...) 11: .local(.Object, ...) 12: callNextMethod(.Object, .Template, ..., setIdentifier = mkScalar(setIdentif 13: eval(call, callEnv) 14: eval(expr, envir, enclos) 15: .nextMethod(.Object, .Template, ..., setIdentifier = mkScalar(setIdentifier 16: validObject(.Object) Selection: line 4 gives a hint that the problem in in line ~ 4694 of the file. I then responded with Selection: 16 Called from: top level Browse[1]> getValidity(getClass("GeneSet")) function (object) { if (any(duplicated(geneIds(object)))) "gene symbols must be unique" else TRUE } <environment: namespace:gseabase=""> Browse[1]> geneIds(object)[which(duplicated(geneIds(object)))] [1] "NM_009369" and then verified that in the original file this is indeed the only line with a duplicated identifier > txt = readLines("c2.all.v4.0.orig.gmt") > fld = strsplit(txt, "\t") > dups = sapply(fld, function(x) any(table(x) != 1)) > which(dups) [1] 4694 The short term solution is to edit c2.all.v4.0.orig.gmt to remove the duplicate entry txt[4694] = sub("NM_009369\t", "", txt[4694]) writeLines(txt, "c2.all.v4.0.orig_MODIFIED_.gmt") the longer term solution is to report the problem to the MSigDB maintainers. Martin > > how to fix it out? > > -- 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. > > ____________________________________________________________________ ____ > devteam-bioc mailing list > To unsubscribe from this mailing list send a blank email to > devteam-bioc-leave at lists.fhcrc.org > You can also unsubscribe or change your personal options at > https://lists.fhcrc.org/mailman/listinfo/devteam-bioc > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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On 09/06/2013 06:17 AM, Martin Morgan wrote: > > txt[4694] = sub("NM_009369\t", "", txt[4694]) > writeLines(txt, "c2.all.v4.0.orig_MODIFIED_.gmt") maybe a better way is to avoid writing to the intermediate file txt = readLines("c2.all.v4.0.orig_MODIFIED_.gmt") ## remove duplicate entry in gene set txt[4694] = sub("NM_009369\t", "", txt[4694]) getGmt(textConnection(txt)) and in this way more tightly coupling the transformation with your analysis. Martin -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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