[Bioc-devel] RFC - annotation packages and ExpressionSets

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