[Bioc-devel] RFC - annotation packages and ExpressionSets
Robert Gentleman
rgentlem at fhcrc.org
Thu Sep 13 18:28:07 CEST 2007
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
--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org
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