[Bioc-devel] will there be a rhesus base level annotation (.db0) package?

M.A. Bijl m.a.bijl at erasmusmc.nl
Wed Mar 18 16:17:16 CET 2009

Dear list,

We are using R and BioC to process and analyze Affy microarray data from 
different species, namely human, mouse and rhesus macaque. I have a 
question concerning the translation of probeset ids to (among other 
things) gene symbols. Everything is fine and peachy using BioC 2.1, we 
are happily using the available packages from BioC (for example 
hgu133plus, mouse4302) and custom cdf packages from the brainarray 
website (hs133phsensg, mamurhesusmamuensg etc). The environment 
structure mapping affy ids to symbols and genenames was easy enough to 
understand and recreate for chiptype 'rhesus' ('missing' in BioC 2.1) 
and the custom cdf's where it was partly unavailable.

While looking into upgrading to BioC 2.3 problems arose. The packages 
mentioned above don't exist anymore and I understand that design 
decision. Fortunately, the procedure for getting annotation data from 
the new .db packages hasn't changed. The underlying data structure 
however changed dramatically.....Packages which are 'missing' are 
rhesus.db and the ENSG custom cdf .db files (version 11) we prefer to 
use. After quickly browsing through the AnnotationDbi and SQLForge 
vignettes I think I should be able to create custom cdf .db files for 
human and mouse chips. However, since rhesus.db0 does not exist, I don't 
see any way to create a rhesus.db package or a custom version (with 
ensembl ids pointing to gene symbols). My guess is that creating 
rhesus.db0 myself is next to impossible....? Will such a package ever be 

Best regards,


B.ICT M.A. Bijl
Erasmus MC
Dept. of Virology, Rm. 17.22a
Dr. Molewaterplein 50
3000 DR Rotterdam
The Netherlands

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