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

Marc Carlson mcarlson at fhcrc.org
Thu Mar 19 16:50:57 CET 2009

Hi Bijl,

I will be able to start working on finding you a solution for this
problem next week.  We have a few organisms backed up that have been
requested that we will need to extend support for and it is most
efficient if I tackle these issues all at once.  Assuming that I succeed
in finding all the source resources I need, we should be able to get
these problems addressed for you within a couple of weeks.  Thanks in
advance for your patience, things are a little hectic right at the
moment with the release currently in progress.


M.A. Bijl wrote:
> 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 available?
> Best regards,
> Maarten
> -- 
> 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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