[BioC] How does BioC map from Probe ID to Entrez Gene?

[John Zhang]

>Which brings me to my question - how exactly does BioC map from Affy
>probe IDs to Entrez Gene IDs? There seems to be thorough documentation
>of how Entrez IDs are mapped to other annotations like Pubmed, GO, etc.
>but not much on how the Entrez Gene ID was mapped from the probe ID in
>the first place.  My cursory "hand" examination tends to side with Affy,
>by BLAST-ing their probe sequences.

BioC takes the GeneBank ids associated with the probes (provided by the 
manufacture) and then maps them to Entrez Gene ids using data from UniGene, 
Entrez Gene, and other available data sources we trust. The Entrez Gene id a 
probe is assigned to is determined by votes from all the sources used. If there 
is no agreement among the sources, we take the smallest Entrez Gene id. 


>
>Any enlightenment would be much appreciated.
>
>Thanks,
>
>Jake
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084