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}}

