Dear All I am using the GOstats package to calculate enriched Gene Ontology terms in a gene set. I followed the steps described in the manual, however for some genes the summary table gives an Odds Ratio equal to "Inf". This always happens when the gene counts and the universe counts are the same. Can someone please explain me this result? See for example: > summary(hgOver_BP)[summary(hgOver_BP)$OddsRatio=="Inf",] GOBPID Pvalue OddsRatio ExpCount Count Size 211 GO:0015985 6.838762e-08 Inf 4.3127788 14 14 212 GO:0015986 6.838762e-08 Inf 4.3127788 14 14 320 GO:0042026 7.645560e-06 Inf 3.0805563 10 10 360 GO:0000028 2.485174e-05 Inf 2.7725007 9 9 361 GO:0000338 2.485174e-05 Inf 2.7725007 9 9 362 GO:0006613 2.485174e-05 Inf 2.7725007 9 9 363 GO:0010388 2.485174e-05 Inf 2.7725007 9 9 404 GO:0009188 8.076815e-05 Inf 2.4644450 8 8 How is the OddsRatio calculated here? According to the definition of Odds Ratio that I know, I don't see why two equal counts should give an infinite number. Many thanks in advance Best regards Moreno > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Italian_Italy.1252 [2] LC_CTYPE=Italian_Italy.1252 [3] LC_MONETARY=Italian_Italy.1252 [4] LC_NUMERIC=C [5] LC_TIME=Italian_Italy.1252 attached base packages: [1] parallel stats graphics grDevices [5] utils datasets methods base other attached packages: [1] org.Hs.eg.db_2.10.1 org.Mm.eg.db_2.10.1 [3] GOstats_2.28.0 graph_1.40.1 [5] Category_2.28.0 GO.db_2.10.1 [7] Matrix_1.1-3 ReactomePA_1.6.1 [9] AnnotationDbi_1.24.0 Biobase_2.22.0 [11] BiocGenerics_0.8.0 RSQLite_0.11.4 [13] DBI_0.2-7 biomaRt_2.18.0 [15] xlsx_0.5.5 xlsxjars_0.6.0 [17] rJava_0.9-6 loaded via a namespace (and not attached): [1] annotate_1.40.1 AnnotationForge_1.4.4 [3] colorspace_1.2-4 dichromat_2.0-0 [5] digest_0.6.4 DO.db_2.7 [7] DOSE_2.0.0 genefilter_1.44.0 [9] ggplot2_0.9.3.1 GOSemSim_1.20.3 [11] graphite_1.8.1 grid_3.0.2 [13] GSEABase_1.24.0 gtable_0.1.2 [15] igraph_0.7.0 IRanges_1.20.7 [17] labeling_0.2 lattice_0.20-29 [19] MASS_7.3-31 munsell_0.4.2 [21] plyr_1.8.1 proto_0.3-10 [23] qvalue_1.36.0 RBGL_1.38.0 [25] RColorBrewer_1.0-5 Rcpp_0.11.1 [27] RCurl_1.95-4.1 reactome.db_1.46.1 [29] reshape2_1.2.2 scales_0.2.3 [31] splines_3.0.2 stats4_3.0.2 [33] stringr_0.6.2 survival_2.37-7 [35] tcltk_3.0.2 tools_3.0.2 [37] XML_3.98-1.1 xtable_1.7-3 =============================== Moreno Colaiacovo Computational Biologist Genomnia srl Via Nerviano, 31/B - 20020 Lainate (MI) Tel. 0293305.711 - Fax 0293305.777 <http: www.genomnia.com=""/> www.genomnia.com moreno.colaiacovo@genomnia.com P Per cortesia, prima di stampare questa e-mail pensate all'ambiente. Please consider the environment before printing this mail note. ----------------------------------------------------------- Il Contenuto del presente messaggio potrebbe contenere informazioni confidenziali a favore dei soli destinatari del messaggio stesso. Qualora riceviate per errore questo messaggio siete pregati di cancellarlo dalla memoria del computer e di contattare i numeri sopra indicati. Ogni utilizzo o ritrasmissione dei contenuti del messaggio da parte di soggetti diversi dai destinatari e da considerarsi vietato ed abusivo. The information transmitted is intended only for the per...{{dropped:10}}

Hi Moreno, The odds ratio is odds of being GO term X | in significant set/odds of being GO term X | not in significant set If all of the genes mapped to GO term X are in the significant set, the odds of being mapped to GO term X and not being in the significant set are zero. Divide by zero, you get Inf. Best, Jim On 4/28/2014 6:42 AM, Moreno Colaiacovo wrote: > Dear All > > > > I am using the GOstats package to calculate enriched Gene Ontology terms in > a gene set. I followed the steps described in the manual, however for some > genes the summary table gives an Odds Ratio equal to "Inf". This always > happens when the gene counts and the universe counts are the same. Can > someone please explain me this result? > > > > See for example: > > > >> summary(hgOver_BP)[summary(hgOver_BP)$OddsRatio=="Inf",] > GOBPID Pvalue OddsRatio ExpCount Count Size > > 211 GO:0015985 6.838762e-08 Inf 4.3127788 14 14 > > 212 GO:0015986 6.838762e-08 Inf 4.3127788 14 14 > > 320 GO:0042026 7.645560e-06 Inf 3.0805563 10 10 > > 360 GO:0000028 2.485174e-05 Inf 2.7725007 9 9 > > 361 GO:0000338 2.485174e-05 Inf 2.7725007 9 9 > > 362 GO:0006613 2.485174e-05 Inf 2.7725007 9 9 > > 363 GO:0010388 2.485174e-05 Inf 2.7725007 9 9 > > 404 GO:0009188 8.076815e-05 Inf 2.4644450 8 8 > > > > How is the OddsRatio calculated here? According to the definition of Odds > Ratio that I know, I don't see why two equal counts should give an infinite > number. > > > > Many thanks in advance > > > > Best regards > > Moreno > > > >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=Italian_Italy.1252 > [2] LC_CTYPE=Italian_Italy.1252 > [3] LC_MONETARY=Italian_Italy.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=Italian_Italy.1252 > > attached base packages: > [1] parallel stats graphics grDevices > [5] utils datasets methods base > > other attached packages: > [1] org.Hs.eg.db_2.10.1 org.Mm.eg.db_2.10.1 > [3] GOstats_2.28.0 graph_1.40.1 > [5] Category_2.28.0 GO.db_2.10.1 > [7] Matrix_1.1-3 ReactomePA_1.6.1 > [9] AnnotationDbi_1.24.0 Biobase_2.22.0 > [11] BiocGenerics_0.8.0 RSQLite_0.11.4 > [13] DBI_0.2-7 biomaRt_2.18.0 > [15] xlsx_0.5.5 xlsxjars_0.6.0 > [17] rJava_0.9-6 > > loaded via a namespace (and not attached): > [1] annotate_1.40.1 AnnotationForge_1.4.4 > [3] colorspace_1.2-4 dichromat_2.0-0 > [5] digest_0.6.4 DO.db_2.7 > [7] DOSE_2.0.0 genefilter_1.44.0 > [9] ggplot2_0.9.3.1 GOSemSim_1.20.3 > [11] graphite_1.8.1 grid_3.0.2 > [13] GSEABase_1.24.0 gtable_0.1.2 > [15] igraph_0.7.0 IRanges_1.20.7 > [17] labeling_0.2 lattice_0.20-29 > [19] MASS_7.3-31 munsell_0.4.2 > [21] plyr_1.8.1 proto_0.3-10 > [23] qvalue_1.36.0 RBGL_1.38.0 > [25] RColorBrewer_1.0-5 Rcpp_0.11.1 > [27] RCurl_1.95-4.1 reactome.db_1.46.1 > [29] reshape2_1.2.2 scales_0.2.3 > [31] splines_3.0.2 stats4_3.0.2 > [33] stringr_0.6.2 survival_2.37-7 > [35] tcltk_3.0.2 tools_3.0.2 > [37] XML_3.98-1.1 xtable_1.7-3 > > > > > > =============================== > > Moreno Colaiacovo > > Computational Biologist > > Genomnia srl > > Via Nerviano, 31/B - 20020 Lainate (MI) > > Tel. 0293305.711 - Fax 0293305.777 > > <http: www.genomnia.com=""/> www.genomnia.com > > moreno.colaiacovo at genomnia.com > > > > P Per cortesia, prima di stampare questa e-mail pensate all'ambiente. > > Please consider the environment before printing this > mail note. > > > > > > > > ----------------------------------------------------------- > Il Contenuto del presente messaggio potrebbe contenere informazioni confidenziali a favore dei > soli destinatari del messaggio stesso. Qualora riceviate per errore questo messaggio siete pregati > di cancellarlo dalla memoria del computer e di contattare i numeri sopra indicati. Ogni utilizzo o > ritrasmissione dei contenuti del messaggio da parte di soggetti diversi dai destinatari e da > considerarsi vietato ed abusivo. > > The information transmitted is intended only for the per...{{dropped:10}} > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099