[BioC] annaffy annotation problem (hgu133plus2)

[Dipl.-Ing. Johannes Rainer]

hi,

i am wondering how the annotation of the Affymetrix chips are done... i 
know how the AnnBuilder package works and i also used it, but as the 
starting point for any annotation is the GenBank id for which the probe 
set codes i would like to know from where this mapping information 
comes. are those packages built using the probe set to genbank mapping 
that can be downloaded from affymetrix, or the (sometimes) newer 
annotation that is available through Affymetrix NetAffx or some other 
source?

I am really interested in this, because we got a little annotation 
problem with the annotation for the hgu133plus2 chip (version 1.7.0). 
one of our interesting genes in our study was the probe set 208078_s_at 
which is mapped using the hgu133plus2 package (and the annotation from 
Affymetrix) to NM_030751 (TCF8). we made real time PCR to confirm its 
regulation but this TCF8 was not regulated at all. so i went back to 
NetAffx tool and saw that Affymetrix gave a new annotation for this 
probe set, all 11 probes perfectly match with the gene NM_173354 
(SNF1LK) (i wonder how Affymetrix could annotate this gene to the TCF8 
gene).

if the annotation packages are built using the downloadable probe set 
to genbank mapping files from Affymetrix (which may never updated and 
corrected for errors by Affymetrix) i believe that there may be more 
annotation errors in this package like the one we found.

cheers, jo