[BioC] athPkgBuilder data source :missing probesets

[Robert Gentleman]

Thomas Girke wrote:
> I would go for the solution that supports a one-to-many relationship
> for the probe-to-locus mappings. This way there is no information loss.
> 

  The problem with that approach is that it will break an awful lot of 
downstream code that believes that these are one-to-one mappings.  We 
really would need a full release cycle (starting in early October) to 
get such a change to work and to minimize the likely negative effects. 
We would also like to be sure that there are good reasons for the 
one-to-many result, it is problematic for other reasons as well.


  best wishes
   Robert



> Thomas
> 
> On Mon 08/14/06 23:25, Nianhua Li wrote:
>> Hi, Tine, Bjorn, Thomas and other Arabidopsis experts,
>>
>> Thanks a lot for the feedbacks. I will get the update done this week if you
>> could help me to solve the following problem :P
>>
>> In TAIR's probe-to-locus mapping file, for example 
>> ftp://ftp.arabidopsis.org/home/tair/
>> Microarrays/Affymetrix/affy_ATH1_array_elements-2006-07-14.txt
>>
>>  some probesets are mapped to >= 1 locus. However, in annotation packages  
>> ath1121501 and ag, all annotations (e.g. agCHRLOC, agENZYME) are indexed by
>> probeset identifier. It assumes a one-to-one mapping between probeset and gene,
>> so that the annotation to a gene is the annotation to a probeset. 
>>
>> How to handle the one probeset to multiple locus mappings? I can think 3
>> possible solutions:
>> 1. pick the "best" locus, but how?
>> 2. mix the annotations to all mapped locus together
>> 3. set to NA
>>
>> Any suggestions are highly appreciated. Many thanks!
>>
>> nianhua
>>
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> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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rgentlem at fhcrc.org