[BioC] Bioconductor Digest, Vol 82, Issue 20

Seth Falcon sfalcon at fhcrc.org
Mon Dec 21 18:28:10 CET 2009


On 12/21/09 9:11 AM, Yue, Chen - BMD wrote:
> Hi Bucher,
>
> Thanks for the information. I got an error after I tried to use KEGG.db. Here is what I did:
>
>> ids<- scan("D:/geneset.txt")
>> ids
>   [1] 944750 944834 944794 944854 947139 947874 944866 945013 944925 945017 945081 945070
>> pathway<- mget(ids,KEGGEXTID2PATHID, ifnotfound = NA)
> Error in .checkKeysAreWellFormed(keys) :
>    keys must be supplied in a character vector with no NAs
>
> Can you help? Thanks!

Looks like your ids are numeric and need to be character.  Can you try:

    mget(as.character(ids), KEGGEXTID2PATHID, ifnotfound = NA)


+ seth

-- 
Seth Falcon
Program in Computational Biology | Fred Hutchinson Cancer Research Center



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