[BioC] Bioconductor data sets - Unigene IDs

Laurent Gautier laurent@cbs.dtu.dk
Thu, 3 Oct 2002 09:08:14 +0200

On Wed, Oct 02, 2002 at 11:33:00PM +0200, Wolfgang Huber wrote:
> >From this it sounds that clusters only ever merge, but from what I
> understand there are also situations in which they may split. Hence, Unigene
> cluster IDs are very useful intermediate IDs for processing data at a given
> time, but they cannot be used as persistent identifiers. And whenever one
> does such processing, one has to make sure that all Unigene-IDs involved
> refer to the same Unigene-Build. Now, to come to the point, I haven't seen
> that information (about the Unigene build) in the data packages on
> Bioconductor, and I would like to suggest to include that information in the
> package data, and to document how to find the information in a prominent
> place, so software using these packages can make sure the Unigene IDs are
> consistent.

I agree with Wolfgang. I am currently working on environments that are
not completely unrelated to the one provided by the Data package and
I would like to attach extra information to the environment.
I would be happy to follow a convention to stick the information to the
Here are few thoughts about that (just in case):
- set a class for 'Data' environment (chipData)
- set an attribute 'cdfName' (to be used with the affy package.
  indicates the chip it corresponds to)
- set an attribute 'releaseDate' or 'bestBefore'
- set an attribute 'size' (memory usage)
- set an attribute 'comments'



> Best regards
> Wolfgang.
> Dr. Wolfgang Huber
> http://www.dkfz.de/abt0840/whuber
> Tel +49-6221-424709
> Fax +49-6221-42524709
> Division of Molecular Genome Analysis
> 69120 Heidelberg
> Germany
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Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
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