[Bioc-devel] Re: [BioC] can't instal MetaData package "mouse4302"

Gordon Smyth smyth at wehi.edu.au
Sun Mar 13 11:16:05 CET 2005

I've moved this to bioc-devel.

At 12:33 PM 13/03/2005, Robert Gentleman wrote:
>Hi Gordon,
>   Thanks for the careful report - we will be looking in to this and see
>what can be resolved. Some issues are due to the move to Seattle
>(hopefully that is mostly resolved now), and some due to the change
>from LocusLink to EntrezGene - and that is more problematic as our
>basic data sources have changed completely.

Thanks, that's great.

I'd really like to have a better understanding of how the annotation 
packages are put together, the critical thing being the mapping of Affy 
probe set IDs to Entrez Gene (Locus Link) IDs. There's some information 
about this at


but it doesn't fully describe the process. I notice that you're not just 
accepting the Affymetrix supplied Locus Link IDs. In your paper with John 
Zhang, http://bioinformatics.oupjournals.org/cgi/reprint/19/1/155, you 
describe a process which accepts the Affymetrix supplied GenBank IDs, and 
then uses a voting of other data sources to map GenBank to Locus Link. Is 
that still the strategy? Is that better than just accepting the Affymetrix 
supplied LL IDs?

Would it be possible to include with each annotation package the code used 
to build it, say in a directory called /build or whatever? The code might 
just be a few calls ot AnnBuilder functions, but it would nice to document it.


>   Best wishes,
>     Robert
>On Mar 11, 2005, at 10:40 PM, Gordon Smyth wrote:
>>At 01:11 PM 12/03/2005, Seth Falcon wrote:
>>>Hi Gordon,
>>>The mouse4302 annotation package is again available.  The version is
>>>1.6.9.  The data is the same as version 1.6.8, the packaging was
>>>modified so that the package is usable on Windows.
>>>Sorry for the delay.
>>>+ seth
>>Hi Seth,
>>Many thanks for this.  I'll update my recent Mouse 430 2.0 analyses
>>with this package.
>>I've compared versions 1.6.5 and 1.6.9 of the mouse4302 annotation
>>package and found somewhat more differences than I expected.

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