[BioC] Annotation parameter of hyperGTest

[Michael Mayhew]

Greetings,

   I am using the GOstats package to identify significant association with GO
terms of a set of "interesting" sequences NOT identified by a microarray.

   As far as I can tell, I have set up the vectors for the gene universe and
"interesting" genes correctly. However, I am not sure what to specify for the
'annotation' parameter of the GOHyperGParams object.

   The vignettes use the "hgu95av2" Affymetrix chip annotation package as an
example. Would be this be appropriate to use if my interesting genes were not
taken from a microarray study?

   If not, is it possible to use some other environment (in the GO library
perhaps)? 

   I have already tried specifying "GOENTREZID2" as the annotation package, but
I receive the following error message and think I am missing something:

        ""Error in get(x, envir, mode, inherits) : variable
"GOENTREZID2ENTREZID" of mode "environment" was not found""

Do I need to specify a new variable for the Entrez IDs?

Any advice would be greatly appreciated on how to set the annotation parameter
for the hyperGTest. 

Thank you.

Michael