 
Hi,

I
was performing a hyperGTest for genes in homo-sapiens. For a set of
input genes, this function returns some 'significant' GO terms. What I
wanted to now do was to co-relate each significant GO term (returned by
this function) with genes (from my set of input genes) associated with
that GO term. However, I think that I may be using the wrong
package/function to get the releveant set of genes.

Currently, what I'm doing is finding the significant GO terms by using the following code:

-----------------------
### 'genes1' are the Entrez IDs of my genes of interest, and 'allGenes' is the universe of Entrez IDs 

 paramsGO <- new("GOHyperGParams", geneIds = genes1,
          universeGeneIds = allGenes, annotation = "org.Hs.eg.db", 
          ontology = "BP", pvalueCutoff = 1, conditional = FALSE, 
          testDirection = "over")

GO <- hyperGTest(paramsGO)
--------------------------
This
gives me a set of significant GO terms. Now, I would like to find which
subset of genes in 'genes1' is associated with each of the significant
GO term. To do this I map all GO terms to their Entrez IDs using the
'org.Hs.eg.db' package using the following:

xx <- as.list(org.Hs.egGO2EG)

to
get a mapping of GO terms to Entrez IDs. I get 6,756 GO terms (isn't
this number small?) that map to at least one Entrez ID. So, from here I
look up which Entrez IDs are associated with my GO term of interest.

My
problem is that often, the GO term from hyperGTest is not associated
with any Entrez ID (using xx <- as.list(org.Hs.egGO2EG) described
above ), i.e. the GO term/ID is not in the list obtained from
'org.Hs.egGO2EG'). For example, the term 'GO:0043284' is thrown up by
hyperGTest, but does not appear to be associated with any Entrez IDs in
the org.Hs.eg.db package. Where could I be going wrong?

I would give a set of genes so that the example is reproducible, but with hundreds of genes the email will get too long!

Thanks for any comments/suggestions. I realize that I'm probably doing something really stupid here....

My sessionInfo() is:
--------------------------------
R version 2.7.2 (2008-08-25) 
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] grid      splines   tools     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1]
gplots_2.6.0         gmodels_2.14.1       gtools_2.4.0        
gdata_2.4.1          Rgraphviz_1.18.1     GOstats_2.6.0       
Category_2.6.0      
 [8] RBGL_1.16.0          annotate_1.18.0     
xtable_1.5-2         graph_1.18.0         PFAM.db_2.2.0       
GO.db_2.2.0          KEGG.db_2.2.0       
[15] org.Hs.eg.db_2.2.0   AnnotationDbi_1.2.0  RSQLite_0.6-8        DBI_0.2-4            genefilter_1.20.0    survival_2.34-1      affy_1.18.0         
[22] preprocessCore_1.2.0 affyio_1.8.0         Biobase_2.0.0       

loaded via a namespace (and not attached):
[1] cluster_1.11.11 MASS_7.2-44    


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