[Bioc-devel] Oddity in hgu133plus2.db?

James MacDonald jmacdon at med.umich.edu
Wed Nov 25 13:08:12 CET 2009

Hi Lasse,

This gene doesn't exist in that table:

> get("CD68", revmap(hgu133plus2SYMBOL))
[1] NA

It just so happens that selecting things the way you did returns an empty ProbeAnnDbBimap, which when converted to character gives you character(0).

> revmap(hgu133plus2SYMBOL)["CD68"]
revmap(SYMBOL) submap for chip hgu133plus2 (object of class "ProbeAnnDbBimap")



>>> Lasse Folkersen <lasse.folkersen at ki.se> 11/25/09 6:40 AM >>>
I know it is a very specific case, but this seems to me like a general error:

in hgu133plus2.db package, using
named character(0)
Now, it may be that annotations change, but isn't it a mistake that
there exists an Rkey entry for the gene which links to nothing?
Usually genes with no known probesets just didn't exist in the
database at all.

Best regards

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