[BioC] Affychip coli asv2 annotation files

Seth Falcon sfalcon at fhcrc.org
Fri Apr 7 16:30:26 CEST 2006

Hi Caroline,

lemerle at embl.de writes:
> I am analysing Affymetrix GeneChips of type coli asv2.
> I wanted to use the "annotate" package but found no appropriate annotation files
> in the bioc repository.
> I then found out about AnnBuilder, but the vignette mentions that for any
> species that are neither human, rat or mouse, AnnBuilder needs to be
> "extended".

The challenge as I understand it, is that AnnBuilder is designed to
pull most of its data from NCBI and for species other than human, rat,
and mouse, there tends not to be enough information available to build
the required mappings between different public data resources.

> The paragraph about AnnBuilder extension is a heading with no
> content in that vignette (the ABPrimer). What is the status of this
> ?  Does someone maybe have such annotation files already that i may
> use?  (If so, could they maybe be added to the bioc repository?)

We'd be more than happy to add such a package if one was contributed.
And thanks for the reminder about the missing section in the
AnnBuilder vignette.


+ seth

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