I should change slightly what I have said. The hgu133plus2.db package in the
new version of BioC has changed quite a bit, and no longer contains much
data. Instead, it is a thin wrapper for the org.Hs.eg.db package.
Since org.Hs.eg.db *does* contain mappings for this symbol, the Rkey exists:
grep("CD68", Rkeys(hgu133plus2SYMBOL), value=T)
[1] "CD68"
But this doesn't mean this gene product is interrogated by the hgu133plus2
chip. The Lkey for this symbol is NA, because a matching probeset is Not
Available on the hgu133plus2 chip.
So the behavior is consistent - there is a Rkey for this symbol, but the
Lkey is NA.
Best,
Jim
Lasse Folkersen wrote:
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