There are some differences between limma(bioconductor) annotations and
Affymetrix annotations because bioconductor and Affymetrix use
methods to obtain the annotations.
Bioconductor uses the RepresentativePublicIdentifier given by
as the starting point for the annotations. Affymetrix currently tries
align the probes to a transcript which it calls the Annotation
and the annotations are those for that transcript. For some probe sets
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
of 5-10%, between one release of
bioconductor annotations and the next, and between one release of
Affymetrix annotations and the next.