[BioC] revmap question

[Robert Gentleman]

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 :-(


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
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org