[BioC] Agilent annotation source

axel.klenk at actelion.com axel.klenk at actelion.com
Thu Feb 4 10:27:50 CET 2010

Dear BioC list and Biocore Data Team,

we are using various Agilent arrays and the recent paper by Gertz et al.
( http://www.biomedcentral.com/1471-2164/10/566 ) made me feel a
little bit uneasy about the annotation provided by that vendor.

As far as I understand, BioC annotation, e.g. in package hgug4112a.db,
is using EntrezGene IDs as keys to retrieve public annotation for a given
EntrezGene entry -- but where does the mapping from Agilent's Oligo ID
to EntrezGene come from?

I have tried to find the answer in the package's reference manual and help
pages but would prefer to be absolutely sure in this case...

Thanks in advance, 

 - axel

P.S., I do not yet have much experience with sequence analysis in BioC
and would also be grateful for pointers to packages that could help me
verify oligo mappings myself.

Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 

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