[Bioc-devel] New 2.1.4 Annotation packages in R-devel branch

[Marc Carlson]

This is an announcement for those of you who care about annotation the 
packages.

I recently released a large number of new annotation packages to the 
development branch.  These packages can be pretty easily spotted by 
their 2.1.4 version numbers.  They are based on the very latest data 
sources that were available on April 2nd 2008.  Please try out packages 
that are of interest to you and please be sure to let me know if you 
find any problems.

Some things to note: this will be the last time we make non sqlite based 
annotation packages for the following organisms:

Human,
Mouse,
Rat,
Fly,
Yeast,
Arabidopsis

The packages that we intend to deprecate should have a warning that pops 
up when you load them.  This is wrapped in a packageStartupMessage(), so 
you can shut this off if it bothers you, but we want you to know that 
you need to migrate to the newer sqlite versions of these packages. 

Also on the deprecation block are KEGG and GO.  Some people have asked 
what to do if they want to use the GO to entrez gene ID mappings that 
have been left out of the newer GO.db package.  If you like these 
mappings you should plan to use an appropriate organism level package.  
Here are the names of some organism level packages:

For human = org.Hs. eg.db
For mouse = org.Mm.eg.db
For rat = org.Rn.eg.db
For yeast = org.Sc.sgd.db
For fly = org.Dm.eg.db

Please note that the annotation packages now have some new stuff in them 
that you may not have noticed before such as ensemble accessions.  This 
is especially true for the organism level packages where we sometimes 
will put additional species specific information such as flybase IDs. 

I hope these help you.


    Marc