[BioC] athPkgBuilder data source :missing probesets

[Thomas Girke]

Nianhua,

I guess in this case, I'd support your second solution:

>> 2. mix the annotations to all mapped loci together

In the future it may make a lot of sense to support one-to-many relationships
on this level. I bet there are a lot of chips from other organisms where
a considerable fraction of probe sets maps to several genes.

Thanks again for doing this!

Best,

Thomas




On Wed 08/16/06 09:42, Tine Casneuf wrote:
> But to me it is hard to think of a way to choose the 'best' locus that 
> is detected by a probeset. And also if you pick 1 of them, it appears as 
> if only 1 is detected by this probeset, while actually there are more. 
> There are I presume not many cases where a measure from these probesets 
> are useful, so you might as well annotate it with 'multiple'.
> 
> tine
> 
> 
> Robert Gentleman wrote:
> 
> >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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> >>>
> >>
> >
> 

-- 
Thomas Girke, Ph.D.
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