[Bioc-devel] Oddity in hgu133plus2.db?

James W. MacDonald jmacdon at med.umich.edu
Wed Nov 25 14:46:35 CET 2009

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.



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
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues 

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