[BioC] ToggleProbe() and Arabidopsis annotation file ath1121501.db.

Marc Carlson mcarlson at fhcrc.org
Wed Dec 15 19:09:52 CET 2010

Hi Song,

For all packages if you don't use toggleProbes() you will not (by
default) get the probes that map to more than one gene.  For most
situations this is probably the behavior that you want.

In the Arabidopsis packages there has been a long standing "prior art"
tradition of always exposing probes that mapped to multiple genes
because of the nature of the organism and the expectations of that
community.  This has never been the case for the other organisms we
support.  However, these days all the packages act the same (we unified
the behavior across all platforms).  So this message was just a warning
to people who expected the Arabidopsis packages to have the old behavior. 


On 12/08/2010 02:03 PM, Song Li wrote:
> Hi All,
> I was loading Arabidopsis ath1121501.db package using some old code to
> check my results from several years back. I got the following message:
> """
> Warning: All Arabidopsis packages now require you to use the
>   toggleProbes() method in order to expose multiple mappings.
> """
> I googled and find in the AnnotationDbi document:
> """
> In many probe packages, some probes are known to map to multiple genes.
> The reasons for this can be biological as happens in the arabidopsis packages,
> """
> My question is:
> 1) What is happening  biologically in the Arabidopsis package?
> 2) Does the warning message means that if I don't use "toggleProbes()"
> I only get probes that map to single gene? Is this true for other
> packages?
> Thanks,
> Song Li

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