[BioC] difference between annotation

Maria Stalteri m.stalteri at mail.cryst.bbk.ac.uk
Fri Dec 15 13:02:04 CET 2006

Hi Gregory,

There are some differences between limma(bioconductor) annotations and
Affymetrix annotations because bioconductor and Affymetrix use different
methods to obtain the annotations.

Bioconductor uses the RepresentativePublicIdentifier given by Affymetrix
as the starting point for the annotations. Affymetrix currently tries to 
align the probes to a transcript which it calls the Annotation Transcript,
and the annotations are those for that transcript. For some probe sets the
different methods assign the probe set to a different gene.

Also, as Michal mentioned, databases such as GenBank are constantly 
changing, and knowledge of the genome is constantly evolving,
so you can expect to find annotation differences, sometimes of the order 
of 5-10%,  between one release of
bioconductor annotations and the next, and between one release of 
Affymetrix annotations and the next.


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