[Bioc-devel] Oddity in hgu133plus2.db?

[Lasse Folkersen]

Ok. I'll put checks for gensymbols linking to NA values for probeset
into my code in the future. Thank you so much for the info.
Lasse

2009/11/25 James W. MacDonald <jmacdon at med.umich.edu>:
> 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
>>>
>>> _______________________________________________
>>> 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
>>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be
> used for urgent or sensitive issues
>