Hi-
I'm trying to analyze some Sorghum NGS transcriptome data using topGO.  The
analysis runs using my custom geneID2GO object and the annFUN.gene2GO
function.  When I run GenTable, however, the results are strange.  For
example, for the GO:0006970 category, the geneID2GO mappings I used only
lists 48 genes annotated to this category, but the GenTable function claims
that 335 genes are annotated and 270 of them are significant.  If I dig
deeper and see what those 335 genes are they do indeed appear to be sorghum
gene IDs; they are all unique and contain my original 48.

I assume that the topGO package is pulling GO-to-gene mappings from
somewhere to find these additional genes, but I cannot find documentation
for it anywhere.  Does anyone know why/how topGO is locating more genes
than I give per GO category and from where they are getting pulled from?
 If my GO annotations are not complete I would like to know, as I thought
they were.

Thanks for the help!
Sincerely,
-Diana
Former USDA researcher
Current USDA consultant

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