[BioC] topGO Fisher test error

[Bruno Giotti [guest]]

Hi list!
Hope someone can help me on this as i've been stuck for a solid couple of days, i've read other posts without finding my issue. I want to perform an enrichment analysis of a list of genes i found from a microarray experiment. The topGOdata object seems to be generated without errors but then i cant perform Fisher test on it.I pasted everything from the very start sorry for that but maybe i did something wrong..

x<-hugene11sttranscriptclusterENTREZID
probekeys<-Lkeys(x)# gene universe (probeset IDs)
x<-hugene11sttranscriptclusterGO
mappedGO<-mappedkeys(x)
probe2GO<-as.list(x[mappedGO]) # list of probe2GO
geneList<-factor(as.integer(probekeys %in% intgenes) # intgenes= my list of interesting probeIDs
names(geneList)<-probekeys
str(geneList)
Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
 - attr(*, "names")= chr [1:33295] "7892501" "7892502" "7892503" "7892504" ...
GOdata<-new("topGOdata", ontology="BP", allGenes= geneList, annot = annFUN.gene2GO, gene2GO=probe2GO)
GOdata
------------------------- topGOdata object -------------------------

 Description:
   -   

 Ontology:
   -  BP 

 33295 available genes (all genes from the array):
   - symbol:  7892501 7892502 7892503 7892504 7892505  ...
   - 898  significant genes. 

 11077 feasible genes (genes that can be used in the analysis):
   - symbol:  7896740 7896754 7896779 7896822 7896921  ...
   - 530  significant genes. 

 GO graph (nodes with at least  1  genes):
   - a graph with directed edges
   - number of nodes = 10376 
   - number of edges = 22233 

------------------------- topGOdata object -------------------------
test.stat <- new("classicCount", testStatistic = GOFisherTest, name = "Fisher test")
resultFisher <- getSigGroups(GOdata, test.stat)
			 -- Classic Algorithm -- 

		 the algorithm is scoring 2569 nontrivial nodes
		 parameters: 
			 test statistic:  Fisher test 
Error in fisher.test(contMat, alternative = "greater") : 
  all entries of 'x' must be nonnegative and finite

This is the error a get...and i dont know what it means. Any help would me much appreciated, sorry if i've been too long!

Many thanks!

Bruno

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] topGO_2.6.0                          SparseM_0.97                        
 [3] GO.db_2.6.1                          graph_1.32.0                        
 [5] hugene11sttranscriptcluster.db_4.0.1 org.Hs.eg.db_2.6.4                  
 [7] RSQLite_0.11.2                       DBI_0.2-5                           
 [9] AnnotationDbi_1.16.19                Biobase_2.14.0                      

loaded via a namespace (and not attached):
[1] grid_2.14.1    IRanges_1.12.6 lattice_0.20-0 tools_2.14.1  



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