Error in HyperGTest with GOHyperGParams class
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@mayte-suarez-farinas-2068
Last seen 9.6 years ago
United States
Hi all, I recently updated to R 2.8. I have a list of significant genes and want to do hypergeometric test to check for over-representing pathways and ontologies. For KEGG it works fine but for GO I got the following error: any help will be appreciated!!! >params <- new("KEGGHyperGParams", geneIds = eids, universeGeneIds = universe, annotation = lib, pvalueCutoff=1) > params2 <- new("GOHyperGParams", geneIds = eids, universeGeneIds = universe, + annotation = lib, ontology = ontology, conditional=cond, pvalueCutoff=1) > hyperGTest(params) Gene to KEGG test for over-representation 116 KEGG ids tested (116 have p < 1) Selected gene set size: 139 Gene universe size: 3166 Annotation package: hgu133a2 > hyperGTest(params2) Error in initialize(value, ...) : invalid names for slots of class "GOHyperGResult": pvalues, oddsRatios, expectedCounts, catToGeneId > str(params) Formal class 'KEGGHyperGParams' [package "Category"] with 8 slots ..@ geneIds : chr [1:394] "3608" "8882" "9948" "163" ... ..@ universeGeneIds : chr(0) ..@ annotation : chr "hgu133a2" ..@ datPkg :Formal class 'AffyDatPkg' [package "Category"] with 1 slots .. .. ..@ name: chr "hgu133a2" ..@ cateogrySubsetIds: NULL ..@ categoryName : chr "KEGG" ..@ pvalueCutoff : num 1 ..@ testDirection : chr "over" > str(params2) Formal class 'GOHyperGParams' [package "Category"] with 10 slots ..@ ontology : chr "BP" ..@ conditional : logi TRUE ..@ geneIds : chr [1:394] "3608" "8882" "9948" "163" ... ..@ universeGeneIds : chr(0) ..@ annotation : chr "hgu133a2" ..@ datPkg :Formal class 'AffyDatPkg' [package "Category"] with 1 slots .. .. ..@ name: chr "hgu133a2" ..@ cateogrySubsetIds: NULL ..@ categoryName : chr "GO" ..@ pvalueCutoff : num 1 ..@ testDirection : chr "over" sessionInfo() R version 2.8.1 (2008-12-22) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] statmod_1.3.8 GOstats_2.8.0 RBGL_1.18.0 Category_2.8.4 annaffy_1.14.0 [6] KEGG.db_2.2.5 GO.db_2.2.5 hgu133a2probe_2.3.0 hgu133plus2.db_2.2.5 hgu133a2.db_2.2.5 [11] hgu133a2cdf_2.3.0 Harshlight_1.12.0 altcdfenvs_2.4.0 hypergraph_1.14.0 graph_1.20.0 [16] Biostrings_2.10.16 IRanges_1.0.12 makecdfenv_1.20.0 affyio_1.10.1 maCorrPlot_1.12.0 [21] lumiHumanIDMapping_1.0.1 lumi_1.8.3 mgcv_1.4-1.1 affyQCReport_1.20.0 RColorBrewer_1.0-2 [26] affyPLM_1.18.1 preprocessCore_1.4.0 simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 [31] genefilter_1.22.0 survival_2.34-1 affy_1.20.2 lumiHumanAll.db_1.4.0 RSQLite_0.7-1 [36] DBI_0.2-4 beadarray_1.10.0 sma_0.5.15 hwriter_1.0 geneplotter_1.20.0 [41] annotate_1.20.1 xtable_1.5-4 AnnotationDbi_1.4.3 lattice_0.17-17 Biobase_2.2.2 [46] limma_2.16.4 loaded via a namespace (and not attached): [1] GSEABase_1.4.0 KernSmooth_2.22-22 Matrix_0.999375-21 XML_2.1-0 cluster_1.11.11 grid_2.8.1
Annotation GO hgu133a2 hgu133plus2 Annotation GO hgu133a2 hgu133plus2 • 1.5k views
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@pankaj-chopra-2741
Last seen 10.3 years ago
Would it be possible to get a reproducible example? thanks! Mayte Suarez-Farinas wrote: > Hi all, > I recently updated to R 2.8. I have a list of significant genes and > want to do hypergeometric test to check for over-representing pathways > and ontologies. > For KEGG it works fine but for GO I got the following error: > > any help will be appreciated!!! > > > > >params <- new("KEGGHyperGParams", geneIds = eids, universeGeneIds = > universe, annotation = lib, pvalueCutoff=1) > > > params2 <- new("GOHyperGParams", geneIds = eids, universeGeneIds = > universe, > + annotation = lib, ontology = ontology, conditional=cond, > pvalueCutoff=1) > > > > hyperGTest(params) > Gene to KEGG test for over-representation > 116 KEGG ids tested (116 have p < 1) > Selected gene set size: 139 > Gene universe size: 3166 > Annotation package: hgu133a2 > > > hyperGTest(params2) > Error in initialize(value, ...) : > invalid names for slots of class "GOHyperGResult": pvalues, > oddsRatios, expectedCounts, catToGeneId > > > str(params) > Formal class 'KEGGHyperGParams' [package "Category"] with 8 slots > ..@ geneIds : chr [1:394] "3608" "8882" "9948" "163" ... > ..@ universeGeneIds : chr(0) > ..@ annotation : chr "hgu133a2" > ..@ datPkg :Formal class 'AffyDatPkg' [package "Category"] > with 1 slots > .. .. ..@ name: chr "hgu133a2" > ..@ cateogrySubsetIds: NULL > ..@ categoryName : chr "KEGG" > ..@ pvalueCutoff : num 1 > ..@ testDirection : chr "over" > > > str(params2) > Formal class 'GOHyperGParams' [package "Category"] with 10 slots > ..@ ontology : chr "BP" > ..@ conditional : logi TRUE > ..@ geneIds : chr [1:394] "3608" "8882" "9948" "163" ... > ..@ universeGeneIds : chr(0) > ..@ annotation : chr "hgu133a2" > ..@ datPkg :Formal class 'AffyDatPkg' [package "Category"] > with 1 slots > .. .. ..@ name: chr "hgu133a2" > ..@ cateogrySubsetIds: NULL > ..@ categoryName : chr "GO" > ..@ pvalueCutoff : num 1 > ..@ testDirection : chr "over" > > > > sessionInfo() > R version 2.8.1 (2008-12-22) > i386-apple-darwin8.11.1 > > locale: > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] statmod_1.3.8 GOstats_2.8.0 > RBGL_1.18.0 Category_2.8.4 annaffy_1.14.0 > [6] KEGG.db_2.2.5 GO.db_2.2.5 > hgu133a2probe_2.3.0 hgu133plus2.db_2.2.5 hgu133a2.db_2.2.5 > [11] hgu133a2cdf_2.3.0 Harshlight_1.12.0 > altcdfenvs_2.4.0 hypergraph_1.14.0 graph_1.20.0 > [16] Biostrings_2.10.16 IRanges_1.0.12 > makecdfenv_1.20.0 affyio_1.10.1 maCorrPlot_1.12.0 > [21] lumiHumanIDMapping_1.0.1 lumi_1.8.3 > mgcv_1.4-1.1 affyQCReport_1.20.0 RColorBrewer_1.0-2 > [26] affyPLM_1.18.1 preprocessCore_1.4.0 > simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 > [31] genefilter_1.22.0 survival_2.34-1 > affy_1.20.2 lumiHumanAll.db_1.4.0 RSQLite_0.7-1 > [36] DBI_0.2-4 beadarray_1.10.0 > sma_0.5.15 hwriter_1.0 geneplotter_1.20.0 > [41] annotate_1.20.1 xtable_1.5-4 > AnnotationDbi_1.4.3 lattice_0.17-17 Biobase_2.2.2 > [46] limma_2.16.4 > > loaded via a namespace (and not attached): > [1] GSEABase_1.4.0 KernSmooth_2.22-22 Matrix_0.999375-21 > XML_2.1-0 cluster_1.11.11 grid_2.8.1 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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