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

[Robert Gentleman]

On Mar 13, 2005, at 2:16 AM, Gordon Smyth wrote:

> 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
>
>   http://www.bioconductor.org/data/annotation.html
>
> 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?
>

  As far as I know - and things are changing rapidly - Affymetrix  
version of things is much better now than it was when we started (at  
least for standard arrays, I am not sure about custom ones) and we are  
going to start to make more use of their data. When we first started  
the answer to your last
question was yes, we were doing much better.

  In any event, Affymetrix does not give mappings to everything we want,  
and so we will still have to do some manipulations and in some cases  
there does seem to be reasonable disagreement (and it is nice to know  
about such cases) - however, as I said, for standard arrays things are  
pretty stable and we are generally only conflicting on fairly obscure  
things.


> 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.

   Well, that is the point of AnnBuilder itself and we do document the  
actual resources and version numbers that have been used, for example  
go:
   ?hgu95av2
and that is pretty explicit. We can look at adding more, but I doubt  
that we can easily give something that is going to be comprehensive.  
The data resources themselves can undergo substantial changes (which  
seems to be what is happening with the mouse data right now) and we are  
struggling to find enough resources to keep up with those changes. Our  
main priority is ensuring that what we produce is accurate - so we do  
appreciate your comments and observations and will try to get things  
running more smoothly.

   I hope that from now on we will be able to provide some basic  
summaries on what has changed when we produce new sets of annotation  
(but again, getting that to work in anything that looks like an  
automatic fashion is non-trivial).

   Robert

> Cheers
> Gordon
>
>>   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.
>>>> Best,
>>>> + 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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| Robert Gentleman              phone: (206) 667-7700                    
          |
| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
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| Fred Hutchinson Cancer Research Center                                 
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| email: rgentlem at fhcrc.org                                              
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