[BioC] error of \"subscript out of bounds\" while applying basicProfile func

[Marc Carlson]

Hi,

It's honestly kind of hard to tell from your post what it is that you 
were doing.  You might want to have a look at the posting guide here:

http://www.bioconductor.org/help/mailing-list/posting-guide/

BUT: if I make the assumption that the IDS you listed are entrez gene 
IDs.  And that you want tair and GO information mapped to them, here is 
how I would do that:

library(org.At.tair.db)
k = c("839235", "838362", "838961", "837091", "837455", "837543")
select( org.At.tair.db, keys=k, columns=c("TAIR","GO"), "ENTREZID")


Hope this helps,


   Marc



On 08/21/2013 01:52 PM, d [guest] wrote:
> While applying basicprofiles on 316 entrez IDs in Arabidopsis it is giving error of "subscript out of bounds".
>
>   -- output of sessionInfo():
>
>> a<-read.table("tair_ids to gene_ids.csv" ,header=TRUE,sep=",")
>   
>> b<-as.character(a[,2])
>> head(b)
> [1] "839235" "838362" "838961" "837091" "837455" "837543"
>
>> h<-basicProfile(b,idType="Entrez",onto ="ANY",level=2,orgPackage="org.At.tair.db",ord=FALSE)
> Error in GOtermslist[[i]] : subscript out of bounds
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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