[BioC] error while using goProfiles package on arabidopsis entrez gene IDs

dd [guest] guest at bioconductor.org
Thu Aug 22 11:07:22 CEST 2013

Hi all,
I was using goProfiles package for functional analysis using a genelist of 316 Arabidopsis entrez gene IDs as shown below in the R command sessionInfo().

- Read a file containing Entrez IDs and TAIR IDs.
- Subset the Entrez IDs and converted to character vector.
- Used the vector as genelist.
-Used goProfiles package function basicProfile for this genelist with organism package of Arabidopsis.

OUTPUT :Error in GOtermslist[[i]] : subscript out of bounds.

Can somebody please help me in finding any mistake I might have done?

Thanks in advance.

 -- output of sessionInfo(): 

Console output :

>> 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.

More information about the Bioconductor mailing list