Hi all,

I was trying to understand the hyperGTest for KEGG, and used the following code:

-----------------------------------------------------------------------------------------------------------
## TEST HYPERGTEST FOR KEGG

library("YEAST")
library("GOstats")
library("GO")

# Convert to a list
xx <- as.list(YEASTGENENAME)
# Remove probes that do not map to any GENENAME
xx <- xx[!is.na(xx)]
if(length(xx) > 0){
   # Gets the gene names for the first five probe identifiers
   xx[1:5]
   # Get the first one
   xx[[1]]
}

## Create gene universe
allGenes <- names(xx)
print(length(allGenes))
geneUniverse <- allGenes[1:800]
for(i in 1:20){
    ## Create random cluster of 13 genes
    geneCluster <- sample(1:800,13,replace=F)
    geneCluster <- geneUniverse[geneCluster]
    print(i)
    print(geneCluster)
    params <- new("KEGGHyperGParams", geneIds = geneCluster,
          universeGeneIds = geneUniverse, annotation = "YEAST",
           pvalueCutoff = 0.1, testDirection = "over")
    hgOver <- hyperGTest(params)
    dfrm <- summary(hgOver)
    #print(dfrm)
}

--------------------------------------------------------------------------------------------------------

The output/error that I got is:

[1] 1
 [1] "YKR067W" "MOF9"    "YDR518W" "YPR074C" "YCL011C" "YCR069W" "YDL104C" "YGR136W" "YAR003W" "YFR013W" "YOR116C" "YDR507C" "YGR167W"
[1] 2
 [1] "YJR112W" "CEN8"    "YPL005W" "YHR081W" "YLR323C" "YBR131W" "YLR347C" "YHR098C" "YOR107W" "YCL027W" "YNR012W" "CRL16"   "YLR329W"
[1] 3
 [1] "YNL327W" "YEL056W" "YNL321W" "YDL111C" "YMR284W" "YLR338W" "YPL008W" "CRL17"   "YEL065W" "YFR027W" "YMR269W" "YPL019C" "YML038C"
Error in numW - numWdrawn : non-numeric argument to binary operator


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My sessionInfo():

> sessionInfo()
R version 2.6.2 (2008-02-08) 
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] splines   tools     stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
 [1] KEGG_2.0.1          GOstats_2.4.0       Category_2.4.0      genefilter_1.16.0   survival_2.34       RBGL_1.14.0         GO.db_2.0.2        
 [8] graph_1.16.1        goTools_1.10.0      annotate_1.16.1     xtable_1.5-2        AnnotationDbi_1.0.6 RSQLite_0.6-8       DBI_0.2-4          
[15] Biobase_1.16.3      GO_2.0.1            hu6800_2.0.1        hgu95a_2.0.1        hgu95av2_2.0.1      hgu133plus2_2.0.1   hgu133b_2.0.1      
[22] hgu133a_2.0.1       som_0.3-4           YEAST_2.0.1         cluster_1.11.10    
> 


thanks!


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