Dear Bioconductor developers and users,

  I'm using GOstats to make the enrichment analysis. And the result show
follows:

> summary(r)
      GOCCID       Pvalue OddsRatio   ExpCount Count Size Term

1 GO:0030131 2.533063e-08 123.95833 0.11423841     5    9 ...
2 GO:0030117 3.487024e-08  52.26471 0.22847682     6   18 ...
3 GO:0048475 3.487024e-08  52.26471 0.22847682     6   18 ...
4 GO:0030118 5.024033e-08  99.11111 0.12693157     5   10 ...

In the result we can see that, the corresponding 'Count' and 'Size'
values.And I use the function geneIdsByCategory(r)[["GO:0030117"]] and
geneIdUniverse(r)[["GO:0030117"]] to get the corresponding genes of 'Count'
and 'Size'.

> geneIdsByCategory(r)[["GO:0030117"]]
[1] "172180" "173121" "173701" "175940" "180713" "186194"

> geneIdUniverse(r)[["GO:0030117"]]
[1] "171860" "171952" "172180" "172553" "173121" "173304" "173701"
[8] "174675" "175376" "175940" "177891" "178078" "178183" "179387"
[15] "180317" "180713" "181163" "186194"

And the same time I use the package org.Ce.egGO to look for the
'GO:0030117' and get the genes in this set, there are only 8 genes in this
set.

> ceGO <- toTable(org.Ce.egGO)
> ceGO[ceGO$go_id == "GO:0030117",]
      gene_id      go_id Evidence Ontology
31601  171860 GO:0030117      IEA       CC
32214  172553 GO:0030117      IEA       CC
32743  173304 GO:0030117      IEA       CC
32927  173701 GO:0030117      IEA       CC
34046  175376 GO:0030117      IEA       CC
34333  175750 GO:0030117      IEA       CC
35977  177891 GO:0030117      IEA       CC
38309  181163 GO:0030117      IEA       CC

What confused me is the different of the genes number between
geneIdUniverse(r)[["GO:0030117"]] and ceGO[ceGO$go_id == "GO:0030117",].
Why they are different from each other? Or some mistake I have made in
those  process?

Wish you can give me a help!

Best,
MiaoYu

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