[BioC] Converting between old and new annotation packages?

Robert Gentleman rgentlem at fhcrc.org
Tue Jun 24 20:41:31 CEST 2008

Jeff Gentry wrote:
> Hi Marc ...
>> The slightly longer answer is that the new style of packages are much 
>> more complex than the old ones because they each contain an actual 
>> sqlite database.  So you could convert from the new style package "down" 
>> into one of the older style packages by querying the database and saving 
>> the results as simple environments.   But you cannot easily go in the 
>> other direction.
> Ah well, figured as much.
>> We already support making new chip packages via SQLForge in the
>> AnnotationDbi package for most major model organisms.  What did you
>> need this for?
> I have a bunch of anno packages for custom spotted array chips from a few
> years back that I was looking to bring into the modern age, and in several
> cases would have to go track down the mapping files and such again ... so
> it seemed worth looking into if there was a way of moving from one to the
> other w/o doing just that.  Its not a big deal, was just trying to figure
> out the path of least resistance.

   Well, you can always get a simple map from your IDs to Entrez gene 
from your current package, and then use that as input, so you don't 
really need to go back to the originals (granted you may want to go back 
as things are likely to have changed since the mapping was done).  But 
at least if you cannot recover files, you can still build something.

   best wishes

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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
rgentlem at fhcrc.org

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