Hello
I am using hyperGTest to look at the GO enrichments. I am confused with the output of the test. For a test, I took the genes in my matrix, and found the those that map to GO:0009790 (there are 8 such genes). Then I ran hyperGTest: using the 8 genes as the input, the genes in my matrix as the universe genes (it is a subset of the genes represented in the hgu133plus2 ). 
When I look at the results, the count field is = 3. I would expect it to be 8. This probably changes the outcome. Am I missing something?
I include the code below as well as the sessionInfo() output.
Any help is appreciated.
Thanks
-burak


universeGeneIds = rownames(myMatrix)
genesWithMyGO = as.list(GOALLENTREZID)$'GO:0009790'
geneIds = intersect(genesWithMyGO, universeGeneIds) # there are 8 genes that are in my matrix with this GO id

> geneIds
[1] "3084"  "4683"  "5801"  "650"   "9314"  "89870" "2139"  "3216"

params = new("GOHyperGParams", geneIds = mygenes, universeGeneIds = universeGeneIds,
             annotation = "hgu133plus2",ontology = "BP", pvalueCutoff = 0.05,conditional = FALSE,testDirection = "over")

# I am using the 8 genes as input

hyp = hyperGTest(params)
t = summary(hyp)
tRep = cbind(t$GOBPID,t$Pvalue,t$OddsRatio,t$ExpCount,t$Count,t$Size,t$Term)
test = tRep[which(tRep[,1]=='GO:0009790'),] # enrichment result with this term
names(test) = c( "GOBPID","Pvalue","OddsRatio","ExpCount","Count","Size","Term")
test

> test
                 GOBPID                  Pvalue               OddsRatio
           "GO:0009790"  "0.000277782573635451"               "37.9125"
               ExpCount                   Count                    Size
    "0.146859903381643"                     "3"                    "19"
                   Term
"embryonic development"
>
>
> sessionInfo()
R version 2.5.0 (2007-04-23)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "methods"   "base"

other attached packages:
hgu133plus2     GOstats    Category  genefilter    survival    annotate
   "1.16.0"     "2.2.6"     "2.2.3"    "1.14.1"      "2.31"    "1.14.1"
         GO        KEGG     Biobase      Matrix     lattice        RBGL
   "1.14.1"     "1.8.1"    "1.14.0" "0.99875-2"    "0.15-4"    "1.12.0"
      graph
   "1.14.2"




       
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