[Bioc-devel] Oddity in hgu133plus2.db?

[Lasse Folkersen]

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
>
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
>