[BioC] GOstats hyperGTest question

[ivan.borozan at utoronto.ca]

Hi all,

I got following results using hyperGTest(params) with a given list of genes

> summary(hgOver)
        GOBPID       Pvalue   OddsRatio    ExpCount Count Size
1  GO:0030185 0.000000e+00  -73.314685  0.02692165     2    1
2  GO:0006067 0.000000e+00 -110.746479  0.05384330     3    2
3  GO:0006069 0.000000e+00 -110.746479  0.05384330     3    2

ect ...


If for example I look at genes that are associated with the first GO  
term (i.e GO:0030185) I get:


> probeSetSummary(hgOver)[[1]]
   EntrezID ProbeSetID selected
1     3043     144221        0
2     3043     148425        0
3     3043    3108408        0
4     3043    5708746        0


My question is how are Counts (in this case Count = 2) in the above  
summary(hgOver) table obtained ?

Looking at probeSetSummary(hgOver)[[1]] I can see one EntrezID  
(EntrezID = 3043) and 4 ProbeSetID associated with this particular  
node (i.e GO:0030185).


R version 2.4.0 (2006-10-03)
i686-redhat-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"     "methods"   "stats"     "graphics"  "grDevices"
[7] "utils"     "datasets"  "base"

other attached packages:
              xtable Hu19K8Build17102006             GOstats            
  Category
             "1.4-3"             "1.1.0"             "2.0.4"            
   "2.0.3"
          genefilter                KEGG                RBGL            
        GO
            "1.12.0"            "1.14.1"            "1.10.0"            
  "1.14.0"
               graph            multtest            survival            
       sma
            "1.12.0"            "1.12.0"              "2.29"            
  "0.5.15"
            annotate             Biobase   human19K601042005
            "1.12.0"            "1.12.1"             "1.1.0"

all the best,
Ivan