Error in summary(hyperGtest)
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Fraser Sim ▴ 270
@fraser-sim-3567
Last seen 9.6 years ago
I am using bioconductor to perform a hyperGtest on GO BP annotations. This code has worked in the past but I am getting a strange error message from the summary method of a hyperGtest-results object. Here's the code: > params = new("GOHyperGParams", + geneIds = as.numeric(geneIds), + universeGeneIds = as.numeric(GeneIDUniverse), annotation = "hgu133plus2", + ontology = "BP", pvalueCutoff = 0.001, conditional = FALSE, + testDirection = "over") > x <- hyperGTest(params) > x Gene to GO BP test for over-representation 652 GO BP ids tested (22 have p < 0.001) Selected gene set size: 74 Gene universe size: 11847 Annotation package: hgu133plus2 > summary(x) Error in if (nrow(df) == 0) { : argument is of length zero Why does summary have this error when it looks like there are 22 categories which should be returned? Here's my sessionInfo() R version 2.9.1 (2009-06-26) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] GOstats_2.10.0 graph_1.22.2 Category_2.10.1 [4] hgu133plus2.db_2.2.11 annaffy_1.16.0 KEGG.db_2.2.11 [7] GO.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 [10] AnnotationDbi_1.6.1 limma_2.18.2 Biobase_2.4.1 loaded via a namespace (and not attached): [1] annotate_1.22.0 genefilter_1.24.2 GSEABase_1.6.0 RBGL_1.20.0 [5] splines_2.9.1 survival_2.35-4 tools_2.9.1 XML_2.3-0 [9] xtable_1.5-5 Thanks, Fraser
Annotation GO hgu133plus2 Annotation GO hgu133plus2 • 919 views
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@james-w-macdonald-5106
Last seen 9 hours ago
United States
Hi Fraser, Fraser Sim wrote: > I am using bioconductor to perform a hyperGtest on GO BP annotations. This > code has worked in the past but I am getting a strange error message from > the summary method of a hyperGtest-results object. > > Here's the code: > >> params = new("GOHyperGParams", > + geneIds = as.numeric(geneIds), > + universeGeneIds = as.numeric(GeneIDUniverse), annotation = > "hgu133plus2", > + ontology = "BP", pvalueCutoff = 0.001, conditional = FALSE, > + testDirection = "over") >> x <- hyperGTest(params) >> x > Gene to GO BP test for over-representation > 652 GO BP ids tested (22 have p < 0.001) > Selected gene set size: 74 > Gene universe size: 11847 > Annotation package: hgu133plus2 >> summary(x) > Error in if (nrow(df) == 0) { : argument is of length zero You shouldn't be seeing an error like that; it indicates that you aren't getting anything at all returned (if df were a 0-rowed data.frame you would just get a warning indicating that fact. The error you see indicates that df was NULL). An example that will replicate this would be nice. You could just give the 74 EG IDs you used by paste("('", paste(as.numeric(geneIds), collapse = "','"), "')", sep = "") And cutting and pasting the output in an email. You could also give the code you used to subset your GeneIDUniverse so we can recreate what you have done. Best, Jim > > Why does summary have this error when it looks like there are 22 categories > which should be returned? > > Here's my sessionInfo() > > R version 2.9.1 (2009-06-26) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] GOstats_2.10.0 graph_1.22.2 Category_2.10.1 > [4] hgu133plus2.db_2.2.11 annaffy_1.16.0 KEGG.db_2.2.11 > [7] GO.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 > [10] AnnotationDbi_1.6.1 limma_2.18.2 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] annotate_1.22.0 genefilter_1.24.2 GSEABase_1.6.0 RBGL_1.20.0 > [5] splines_2.9.1 survival_2.35-4 tools_2.9.1 XML_2.3-0 > [9] xtable_1.5-5 > > Thanks, > Fraser > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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Here are the geneIds... > paste("('", paste(as.numeric(geneIds), collapse = "','"), "')", sep = "") [1] "('5906','3433','51191','91543','6999','3434','8638','10561','3627','1 0964', '9636','54809','8339','8344','3437','2537','8346','85441','85236','641 08','9 3082','11274','3013','5610','85439','10866','4061','8345','222171','10 610',' 55008','23586','10417','8343','51251','8519','3017','6890','129607','2 4138', '7776','51129','57568','55603','2048','10111','3431','152926','197135' ,'8366 6','51513','4599','54739','167227','10486','8351','116071','54897','14 71','7 903','6772','9881','4938','4600','147645','55337','8367','64135','1575 74','9 1351','4940','219285','87178','57714','6773','3456','4741','94240','55 601',' 54328','26047','9068','3620','4747','85352','26002','55384','6332','53 59','8 5462','4343','84166','54625','8347','23767','3665','27324','8038','485 6','57 674','84628','10673','4939')" > And this is how I generate my GeneIDUniverse > GeneIDUniverse = unique(unlist(mget(featureNames(eset), hgu133plus2ENTREZID ))) > GeneIDUniverse = GeneIDUniverse[!is.na(GeneIDUniverse)] Thanks, Fraser -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Monday, July 13, 2009 4:07 PM To: Fraser Sim Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Error in summary(hyperGtest) Hi Fraser, Fraser Sim wrote: > I am using bioconductor to perform a hyperGtest on GO BP annotations. This > code has worked in the past but I am getting a strange error message from > the summary method of a hyperGtest-results object. > > Here's the code: > >> params = new("GOHyperGParams", > + geneIds = as.numeric(geneIds), > + universeGeneIds = as.numeric(GeneIDUniverse), annotation = > "hgu133plus2", > + ontology = "BP", pvalueCutoff = 0.001, conditional = FALSE, > + testDirection = "over") >> x <- hyperGTest(params) >> x > Gene to GO BP test for over-representation > 652 GO BP ids tested (22 have p < 0.001) > Selected gene set size: 74 > Gene universe size: 11847 > Annotation package: hgu133plus2 >> summary(x) > Error in if (nrow(df) == 0) { : argument is of length zero You shouldn't be seeing an error like that; it indicates that you aren't getting anything at all returned (if df were a 0-rowed data.frame you would just get a warning indicating that fact. The error you see indicates that df was NULL). An example that will replicate this would be nice. You could just give the 74 EG IDs you used by paste("('", paste(as.numeric(geneIds), collapse = "','"), "')", sep = "") And cutting and pasting the output in an email. You could also give the code you used to subset your GeneIDUniverse so we can recreate what you have done. Best, Jim > > Why does summary have this error when it looks like there are 22 categories > which should be returned? > > Here's my sessionInfo() > > R version 2.9.1 (2009-06-26) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] GOstats_2.10.0 graph_1.22.2 Category_2.10.1 > [4] hgu133plus2.db_2.2.11 annaffy_1.16.0 KEGG.db_2.2.11 > [7] GO.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 > [10] AnnotationDbi_1.6.1 limma_2.18.2 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] annotate_1.22.0 genefilter_1.24.2 GSEABase_1.6.0 RBGL_1.20.0 > [5] splines_2.9.1 survival_2.35-4 tools_2.9.1 XML_2.3-0 > [9] xtable_1.5-5 > > Thanks, > Fraser > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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> p <- new("GOHyperGParams", geneIds=as.numeric(geneIds), universeGeneIds=as.numeric(GeneIDUniverse), annotation="hgu133plus2.db", ontology="BP", pvalueCutoff=0.001, conditional=F, testDirection="over") > hyp <- hyperGTest(p) > hyp Gene to GO BP test for over-representation 652 GO BP ids tested (22 have p < 0.001) Selected gene set size: 74 Gene universe size: 12592 Annotation package: hgu133plus2 > summary(hyp) GOBPID Pvalue OddsRatio ExpCount Count Size 1 GO:0009615 6.709096e-13 26.431053 0.60530496 12 103 2 GO:0051707 9.964367e-12 15.220988 1.19297967 14 203 3 GO:0009607 1.123924e-10 11.235085 1.71601017 15 292 4 GO:0051704 3.441994e-08 6.672310 3.01477128 16 513 5 GO:0006955 2.755437e-06 4.963045 3.67296696 15 625 6 GO:0050896 7.513094e-06 3.011330 14.39215375 31 2449 7 GO:0006952 1.018216e-04 4.187715 3.32036213 12 565 8 GO:0019441 1.018268e-04 347.694444 0.01763024 2 3 9 GO:0002376 1.485646e-04 3.433529 5.15978399 15 878 10 GO:0045110 2.028774e-04 173.833333 0.02350699 2 4 11 GO:0006569 3.368410e-04 115.879630 0.02938374 2 5 12 GO:0042436 3.368410e-04 115.879630 0.02938374 2 5 13 GO:0046218 3.368410e-04 115.879630 0.02938374 2 5 14 GO:0060052 3.368410e-04 115.879630 0.02938374 2 5 15 GO:0006334 3.917094e-04 12.948571 0.34672808 4 59 16 GO:0052547 4.451811e-04 12.492231 0.35848158 4 61 17 GO:0044419 5.214595e-04 5.484628 1.41629606 7 241 18 GO:0031497 5.348740e-04 11.864762 0.37611182 4 64 19 GO:0006576 6.367334e-04 11.297052 0.39374206 4 67 20 GO:0034728 6.735437e-04 11.119643 0.39961881 4 68 21 GO:0006568 7.019905e-04 69.516667 0.04113723 2 7 22 GO:0045109 9.324263e-04 57.925926 0.04701398 2 8 Term 1 response to virus 2 response to other organism 3 response to biotic stimulus 4 multi-organism process 5 immune response 6 response to stimulus 7 defense response 8 tryptophan catabolic process to kynurenine 9 immune system process 10 intermediate filament bundle assembly 11 tryptophan catabolic process 12 indole derivative catabolic process 13 indolalkylamine catabolic process 14 neurofilament cytoskeleton organization 15 nucleosome assembly 16 regulation of peptidase activity 17 interspecies interaction between organisms 18 chromatin assembly 19 biogenic amine metabolic process 20 nucleosome organization 21 tryptophan metabolic process 22 intermediate filament organization > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] GO.db_2.2.11 GOstats_2.10.0 graph_1.22.2 [4] Category_2.10.1 hgu133plus2.db_2.2.11 RSQLite_0.7-1 [7] DBI_0.2-4 AnnotationDbi_1.6.1 Biobase_2.4.1 loaded via a namespace (and not attached): [1] annotate_1.22.0 genefilter_1.24.2 GSEABase_1.6.1 RBGL_1.20.0 [5] splines_2.9.0 survival_2.35-4 tools_2.9.0 XML_2.5-1 [9] xtable_1.5-5 Have you tried something as simple as restarting R? Best, Jim Fraser Sim wrote: > Here are the geneIds... > >> paste("('", paste(as.numeric(geneIds), collapse = "','"), "')", sep = "") > [1] > "('5906','3433','51191','91543','6999','3434','8638','10561','3627', '10964', > '9636','54809','8339','8344','3437','2537','8346','85441','85236','6 4108','9 > 3082','11274','3013','5610','85439','10866','4061','8345','222171',' 10610',' > 55008','23586','10417','8343','51251','8519','3017','6890','129607', '24138', > '7776','51129','57568','55603','2048','10111','3431','152926','19713 5','8366 > 6','51513','4599','54739','167227','10486','8351','116071','54897',' 1471','7 > 903','6772','9881','4938','4600','147645','55337','8367','64135','15 7574','9 > 1351','4940','219285','87178','57714','6773','3456','4741','94240',' 55601',' > 54328','26047','9068','3620','4747','85352','26002','55384','6332',' 5359','8 > 5462','4343','84166','54625','8347','23767','3665','27324','8038','4 856','57 > 674','84628','10673','4939')" > > And this is how I generate my GeneIDUniverse > >> GeneIDUniverse = unique(unlist(mget(featureNames(eset), > hgu133plus2ENTREZID ))) >> GeneIDUniverse = GeneIDUniverse[!is.na(GeneIDUniverse)] > > Thanks, > Fraser > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: Monday, July 13, 2009 4:07 PM > To: Fraser Sim > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Error in summary(hyperGtest) > > Hi Fraser, > > Fraser Sim wrote: >> I am using bioconductor to perform a hyperGtest on GO BP annotations. This >> code has worked in the past but I am getting a strange error message from >> the summary method of a hyperGtest-results object. >> >> Here's the code: >> >>> params = new("GOHyperGParams", >> + geneIds = as.numeric(geneIds), >> + universeGeneIds = as.numeric(GeneIDUniverse), annotation = >> "hgu133plus2", >> + ontology = "BP", pvalueCutoff = 0.001, conditional = FALSE, >> + testDirection = "over") >>> x <- hyperGTest(params) >>> x >> Gene to GO BP test for over-representation >> 652 GO BP ids tested (22 have p < 0.001) >> Selected gene set size: 74 >> Gene universe size: 11847 >> Annotation package: hgu133plus2 >>> summary(x) >> Error in if (nrow(df) == 0) { : argument is of length zero > > You shouldn't be seeing an error like that; it indicates that you aren't > getting anything at all returned (if df were a 0-rowed data.frame you > would just get a warning indicating that fact. The error you see > indicates that df was NULL). > > An example that will replicate this would be nice. You could just give > the 74 EG IDs you used by > > paste("('", paste(as.numeric(geneIds), collapse = "','"), "')", sep = "") > > And cutting and pasting the output in an email. You could also give the > code you used to subset your GeneIDUniverse so we can recreate what you > have done. > > Best, > > Jim > > >> Why does summary have this error when it looks like there are 22 > categories >> which should be returned? >> >> Here's my sessionInfo() >> >> R version 2.9.1 (2009-06-26) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] GOstats_2.10.0 graph_1.22.2 Category_2.10.1 >> [4] hgu133plus2.db_2.2.11 annaffy_1.16.0 KEGG.db_2.2.11 >> [7] GO.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 >> [10] AnnotationDbi_1.6.1 limma_2.18.2 Biobase_2.4.1 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.22.0 genefilter_1.24.2 GSEABase_1.6.0 RBGL_1.20.0 > >> [5] splines_2.9.1 survival_2.35-4 tools_2.9.1 XML_2.3-0 > >> [9] xtable_1.5-5 >> >> Thanks, >> Fraser >> >> _______________________________________________ >> 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 > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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