[BioC] GO annotation/analysis for ath1121501

[Ann Hess]

I am working with data from ath1121501 (arabidopsis) arrays and I would 
like to do the following:

1.  Subset a list of genes based on GO terms.  For example, how many 
(and which) a given list belong to MF=metabolism.
2.  Create a pie chart of the distribution of GO terms for my list.
3.  Find statistically over-represented GO terms.
4.  Find pathway information for my list.

As simple as goal #1 appears to be, I am not sure how to subset a list by 
GO term.  I am not even sure what GO annotation is available for 
ath1121501 in BioConductor.

In an attempt to accomplish goal #2, I tried using the function 
ontoCompare from the goTools package, but got an error:
>length(DEGList)
[1] 1881
>res<-ontoCompare(DEGList,probeType="ath1121501",plot=TRUE)
[1] "Starting ontoCompare..."
Error in as.vector(x, mode) : invalid argument 'mode'

In an attempt to accomplish goal #3, I tried using the GoHyperG function 
from the GOstats package, but the locus link ID information does not 
appear to be available for ath1121501 (this has been addressed in previous 
postings).  Are there alternatives that can be used for ath1121501?

I was hoping to use the biomaRt package to get pathway information, but it 
doesn't look like it contains annotation for arabidopsis.

Any suggestions would be sincerely appreciated!

Ann