[BioC] how does an annotation package handle ambigious probe set id mappings

Andrew Yee yee at post.harvard.edu
Mon Oct 19 17:27:28 CEST 2009

Apologies if this has been asked before, but how does an annotation
package handle an ambiguous probe set ID mapping?

Take for example the Affymetrix chip U133X3P.

When I use the annotation for this chip for probe set ID
1552641_3p_s_at, it returns only one match:

> library('u133x3p.db')
> mget('1552641_3p_s_at', env=u133x3pSYMBOL)
[1] "ATAD3B"
> mget('1552641_3p_s_at', env=u133x3pENTREZID)
[1] "83858"

However, when I search Affymetrix, with:


it states that it ambiguously maps to three gene symbols, ATAD3A,
ATAD3B, and LOC732419.

How does the annotation package determine which gene symbol it should map to?


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