[BioC] athPkgBuilder data source :missing probesets

[Thomas Girke]

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.

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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-- 
Thomas Girke, Ph.D.
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