[BioC] athPkgBuilder data source :missing probesets

[Tine Casneuf]

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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> >
>