Thanks Marc and James, this discussion has been very informative!
Andrew

On Mon, Oct 19, 2009 at 1:53 PM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Thank you Jim,
>
> The probeset is not displayed in the regular mappings precisely because
> it maps to multiple things.  Because it is of ambiguous assignment, most
> people will probably want to avoid it the majority of the time.  Also,
> legacy code that depends on getting one value back for such operations
> needs to be able to continue working.  However, as you have so carefully
> illustrated, you can now get the complete data for any mapping by using
> toggleProbes().  There are 3 settings for any mapping that can be set
> using toggleProbes: "all" which gives you every mapping regardless of
> what it is, "multiple" which only exposes mappings where many probes map
> to the same item, and "single" which is the default and which will
> expose only those probe IDs that have been assigned by the manufacturer
> to a single gene.  So if you don't use "all" then the troublesome
> ambiguously assigned probes will not be represented in the mapping (ie.
> you will get an NA).  The majority of the time, probes are assigned to a
> single gene and so normally most things are represented just fine by
> "single".  This default has the side benefit that it shields you from
> those probes where the manufacturer is less than certain about the
> identity.  But for those cases where there are multiple genes assigned
> to a probe or probeset, you can now also get all the assignments out if
> you wish (or just the troublesome ones if you want to focus on them) so
> that you can make a guess about which one you think it is you have
> actually measured.
>
>
>  Marc
>
>
>
>
> James W. MacDonald wrote:
> > Hi Andrew,
> >
> > Andrew Yee wrote:
> >> Apologies if this has been asked before, but how does an annotation
> >> package handle an ambiguous probe set ID mapping?
> >>
> >> Take for example the Affymetrix chip U133X3P.
> >>
> >> When I use the annotation for this chip for probe set ID
> >> 1552641_3p_s_at, it returns only one match:
> >>
> >>> library('u133x3p.db')
> >>> mget('1552641_3p_s_at', env=u133x3pSYMBOL)
> >> $`1552641_3p_s_at`
> >> [1] "ATAD3B"
> >>> mget('1552641_3p_s_at', env=u133x3pENTREZID)
> >> $`1552641_3p_s_at`
> >> [1] "83858"
> >>
> >> However, when I search Affymetrix, with:
> >>
> >>
> https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=U133_X3P:1552641_3P_S_AT
> >>
> >>
> >> it states that it ambiguously maps to three gene symbols, ATAD3A,
> >> ATAD3B, and LOC732419.
> >>
> >> How does the annotation package determine which gene symbol it should
> >> map to?
> >
> > In the past we just used the first probeset ==> Entrez Gene ID
> > mapping. However, in the soon to be released BioC 2.5 annotation
> > packages all the mappings are included (thanks to Marc Carlson).
> >
> > > tmp <- toggleProbes(u133x3pENTREZID, "all")
> > > get('1552641_3p_s_at', tmp)
> > [1] "55210"  "732419" "83858"
> > > tmp2 <- toggleProbes(u133x3pSYMBOL, "all")
> > > get('1552641_3p_s_at', tmp2)
> > [1] "ATAD3A"    "LOC732419" "ATAD3B"
> >
> > Oddly enough, this probeset isn't mapped in the 'regular' mappings:
> >
> > > get('1552641_3p_s_at', u133x3pENTREZID)
> > [1] NA
> > > get('1552641_3p_s_at', u133x3pSYMBOL)
> > [1] NA
> >
> > Marc?
> >
> > > sessionInfo()
> > R version 2.10.0 Under development (unstable) (2009-09-21 r49780)
> > i386-pc-mingw32
> >
> > locale:
> > [1] LC_COLLATE=English_United States.1252
> > [2] LC_CTYPE=English_United States.1252
> > [3] LC_MONETARY=English_United States.1252
> > [4] LC_NUMERIC=C
> > [5] LC_TIME=English_United States.1252
> >
> > attached base packages:
> > [1] stats     graphics  grDevices datasets  utils     methods   base
> >
> > other attached packages:
> > [1] u133x3p.db_2.3.5     org.Hs.eg.db_2.3.4   RSQLite_0.7-2
> > [4] DBI_0.2-4            AnnotationDbi_1.7.17 Biobase_2.5.6
> >
> > loaded via a namespace (and not attached):
> > [1] tools_2.10.0
> > >
> >
> > Best,
> >
> > Jim
> >
> >
> >>
> >> Thanks,
> >> Andrew
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
>

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