[BioC] revmap question

[James W. MacDonald]

Robert Gentleman wrote:
> Hi Raffaele,
>   The first looks like a bug, there are some oddities, but mostly it is 
> the rather cute way that R mangles names...
> 
>  > rv = revmap(hgu133plus2ENTREZID)
>  > rv[["1"]]
> [1] "229819_at"
>  > rv[["100"]]
> [1] "204639_at"   "216705_s_at"
>  > rv[["1000"]]
> [1] "203440_at"   "203441_s_at"
> 
>  and you can then do the looping explicitly, this also solves your 
> second problem.
> 
>  I don't know how "1556117_at" got picked up, that does look wrong and 
> we will need to look in to it.
> 
>  > hgu133plus2ENTREZID$"1556117_at"
> [1] NA
> 
> and for "237305_at", I also get an NA :-(

It's a version issue. The hgu133plus2.db package in the current release 
of BioC has these two probesets mapped, but they no longer appear to be 
mapped in the upcoming release.

Best,

Jim


> 
> 
> best wishes
>   Robert
> 
> 
> rcaloger wrote:
>> Hi,
>> I  found very interesting the possibility of using reversing the 
>> mapping by revmap in the XXXX.db annotation databases.
>>
>> However, I have two problems:
>> 1) if  I use:
>> egs <- c("1", "100", "1000")
>> unlist(mget(egs, revmap(hgu133plus2ENTREZID)))
>>
>> I am getting not only the probesets associated to the three EGs:
>>            1          1001          1002          1003         10001
>>  "229819_at"  "1556117_at"   "204639_at" "216705_s_at"   "203440_at"
>>        10002         10003
>> "203441_s_at"   "237305_at"
>> There is any possibility to avoid this problem?
>>
>> 2) if in the egs vector is present an eg (6333) that is not present in 
>> the annotation database I get the following error:
>> egs <- c("1", "100", "1000", "6333")
>> unlist(mget(egs, revmap(hgu133plus2ENTREZID)))
>>
>> Error in .checkKeys(value, Rkeys(x), x at ifnotfound) :
>>  value for "6333" not found
>>
>> There is any possibility to make a query that simply avoid the 
>> unmapped keys?
>>
>>
>> Many thanks
>> Raffaele
>>
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662