sessionInfo()
R version 2.4.0 (2006-10-03)
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"     "methods"   "stats"     "graphics" 
"grDevices" "utils"     "datasets"  "base"

other attached packages:
ath1121501    GOstats   Category 
genefilter   survival       KEGG       RBGL   annotate         GO    Biobase
   "1.14.0"    "2.0.4"    "2.0.3"   "1.12.0"     "2.29"   "1.14.1" 
"1.10.0"   "1.12.0"   "1.14.1"   "1.12.2"
      graph
   "1.12.0"

Here is the output table:  Blue - Count > size,    Red - Count=size

         GOBPID  Pvalue  OddsRatio       ExpCount        Count   Size    Term
1       GO:0006108      0.00    -42.65  0       3       2.00 
malate metabolism
2       GO:0006768      0.00    -28.13  0       2       1.00 
biotin metabolism
3       GO:0009102      0.00    -28.13  0       2       1.00 
biotin biosynthesis
4       GO:0042548      0.00    -28.13  0       2       1.00 
regulation of photosynthesis, light reaction
5       GO:0005513      0.00    -42.65  0       3       2.00 
detection of calcium ion
6       GO:0009865      0.00    -28.13  0       2       1.00 
pollen tube adhesion
7       GO:0009875      0.00    -28.13  0       2       1.00 
pollen-pistil interaction
8       GO:0010109      0.00    -28.13  0       2       1.00 
regulation of photosynthesis
9       GO:0009593      0.00    -42.65  0       3       2.00 
detection of chemical stimulus
10      GO:0043467      0.00    -28.13  0       2       1.00 
regulation of generation of precursor metabolites and energy
11      GO:0019953      0.00    72.56   0       5       6.00 
sexual reproduction
12      GO:0009582      0.00    Inf     0       3       3.00 
detection of abiotic stimulus
13      GO:0051606      0.00    Inf     0       3       3.00 
detection of stimulus
14      GO:0006790      0.00    14.32   1       4       8.00 
sulfur metabolism
15      GO:0006100      0.00    42.59   0       3       4.00 
tricarboxylic acid cycle intermediate metabolism
16      GO:0043648      0.00    42.59   0       3       4.00 
dicarboxylic acid metabolism
17      GO:0006767      0.00    9.53    1       4       10.00 
water-soluble vitamin metabolism
18      GO:0006766      0.00    8.16    1       4       11.00 
vitamin metabolism
19      GO:0006885      0.00    Inf     0       2       2.00 
regulation of pH
20      GO:0001666      0.00    Inf     0       2       2.00 
response to hypoxia
21      GO:0009860      0.00    Inf     0       2       2.00 
pollen tube growth
22      GO:0031323      0.01    2.53    6       13      90.00 
regulation of cellular metabolism
23      GO:0019222      0.01    2.53    6       13      90.00 
regulation of metabolism
24      GO:0042592      0.01    6.34    1       4       13.00   homeostasis


At 03:02 PM 12/11/2006, Seth Falcon wrote:
>Hi Naomi,
>
>Naomi Altman <naomi@stat.psu.edu> writes:
> > I am getting some rather odd "OddsRatio" numbers in my GOstat
> > tables.  In particular, I seem to be getting "Inf" whenever
> > "Observed"="Size".  This does not seem to be right, unless "Size" is
> > the number of hits in the union of the test and nontest set.  But if
> > that is the case, then "Size" should always be greater than or equal
> > to "Observed" and that is not the case.
>
>Hmm, I will certainly look into this.  Can you provide some
>sessionInfo() information?
>
>The "Size" column is the number of genes annotated at the given GO
>term (where genes are restricted to the defined gene universe).  You
>are right that Size should always be greater or equal to the observed
>count.  Jim found a bug relating to this which I fixed.  If you don't
>already have Category 2.0.3 and GOstats 2.0.4, could you try upgrading
>(via biocLite) and let me know if you still see the problem?
>
>+ seth

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

	[[alternative HTML version deleted]]

