[Bioc-devel] RFC - annotation packages and ExpressionSets
Christian.Kohler at klinik.uni-regensburg.de
Tue Jun 17 15:03:40 CEST 2008
Robert Gentleman wrote:
> Hi all,
> As most of you are probably aware in the 2.1 release we will be
> introducing new variants of (almost) all annotation packages. For the
> 2.1 release, at least the naming scheme will be
> hgu95av2, for environment based packages
> hgu95av2.db, for database variants.
> But, we have no intention of maintaining the environment based
> variants (and they may indeed go away by 2.2).
> So this suggests that in the 2.2 release we would then move to
> hgu95av2, for database variants
> hgu95av2.env for environment based ones.
> An alternative is to simply retain the hgu95av2.db scheme (but that
> gets a bit ugly).
> Where things might become problematic is the interaction with
> ExpressionSets, where we have (and often use) the annotation slot.
> I propose that we modify the accessor function to return the .db name,
> for this release and that we try and track down all direct access via @
> in the code base and replace it with use of the accessor function.
sorry for reviving this rather old post, but I am interested in how the
future plan concerning the notation of annotation packages will look like.
At the moment, a 'Deprecation warning' appears while loading the
environment based annotation packages and the use of the *.db*
equivalent is recommended.
Will the *.db* nomenclature endure or will the *.env* notation be
introduced in one of the upcoming releases?
I mean, it is a bit cumbersome to change your analysis-scripts over and
over again :-)
Thanks a lot for any advice.
Institute of Functional Genomics
University of Regensburg (BioPark I)
D-93147 Regensburg (Germany)
Tel. +49 941 943 5055
Fax +49 941 943 5020
christian.kohler at klinik.uni-regensburg.de
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