[BioC] revmap question

rcaloger raffaele.calogero at gmail.com
Tue Oct 7 10:00:29 CEST 2008

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 

Many thanks


Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705417
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
www:   http://www.bioinformatica.unito.it
Info: http://publicationslist.org/raffaele.calogero

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