[Bioc-devel] RFC - annotation packages and ExpressionSets

[Christian Kohler]

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.
>
>   Comments?
>
>   Robert
>
>   

Dear list,

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.

Best
    Christian

-- 

Christian Kohler
Institute of Functional Genomics
Computational Diagnostics
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