[Bioc-devel] Oddity in hgu133plus2.db?

[James MacDonald]

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")

Best,

Jim


>>> 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
as.character(revmap(hgu133plus2SYMBOL)["CD68"])
returns
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
Lasse

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