[BioC] Annotation and gene ontology for a mosquito array

[Amy Mikhail]

Dear list,

I am using a 2-colour cDNA whole genome array for Anopheles gambiae
(mosquito).  The .gal file only has ensembl gene and transcript IDs for
each spot; in addition since the chip was made, a number of the genes on
it have been removed from ensembl as they were incorrectly identified or
thought to be bacterial contaminants.  The providers of the chip are
currently updating the annotation; in the meantime, however, I would like
to know:

How can I used the current ensembl gene list for An. gambiae to:

(a) filter out (remove) those genes from the limma toptables that are no
longer in the database, and;

(b) link gene ontology information to all the genes on the array that are
still listed in the current version of the ensembl database.

Appologies if this is a relatively straightforward thing to do - I have
not tried using annotate or GO before and also not sure what package would
be appropriate to use?

Looking forward to any suggestions,

Regards,
Amy


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Amy Mikhail
Research student
University of Aberdeen
Zoology Building
Tillydrone Avenue
Aberdeen AB24 2TZ
Scotland
Email: a.mikhail at abdn.ac.uk
Phone: 00-44-1224-272880 (lab)