[Bioc-devel] Oddity in hgu133plus2.db?
I see. Its just when genes doesn't exist in a table they usually gives
error messages, like this:
get("whatever", revmap(hgu133plus2SYMBOL))
Error in .checkKeys(value, Rkeys(x), x at ifnotfound) :
value for "whatever" not found
instead of NA. When asking for existence
"CD68" %in% Rkeys(hgu133plus2SYMBOL)
it does gives TRUE
So I thought it could have been a bug or un-wanted behaviour. But
thanks for your answer.
Lasse
2009/11/25 James MacDonald <jmacdon at med.umich.edu>:
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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