[BioC] athPkgBuilder data source :missing probesets

[Nianhua Li]

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