[BioC] problem with hyperGTest and ath1121501?

[Seth Falcon]

Martin Olivier <martinol at ensam.inra.fr> writes:
> I want to use the function hyperGTest on arabidopsis data, but it seems
> that there is a little bug
> in this function. This is an example that gives me an error message
> (hereafter, allegenes is a vector
> of selected genes)
>
> genesel<-c("AT1G55530", "AT5G19770" ,"AT4G10840")

These look like gene symbols.  For Affy chip annotation packages, the
"primary key" is the probe set ID and that is what needs to be
specified as geneID when creating the GOHyperGParams object.

I will try to add more detail to the documentation, as I realize that
"geneID" is not clear -- in a sense it is purposely general because
the function works with other anno pkgs (eg, YEAST) where the primary
key is not a probeset ID.

Now you may have worse problems than that because I don't see any of
the three symbols you listed above in the ath1121501SYMBOL
environment.  You will have a hard time find appropriate probeset IDs
in this case :-P

> The different versions I use are :
> R version 2.4.0
> ath1121501' version 1.14.0
> GOstats' version 2.0.2
> GO version 1.14.0

It is easier and more accurate to paste in the output of the
sessionInfo() function.

Cheers,

+ seth