[BioC] simple biomaRt query

[James W. MacDonald]

Hi Galina,


Glazko, Galina wrote:
> Dear list,
> 
>  
> 
> I am trying to do very simple query using BiomaRt:
> 
> library(biomaRt)
> 
> ensembl=useMart('ensembl')
> 
> ensembl= useDataset('hsapiens_gene_ensembl',mart=ensembl)
> 
> ..
> 
>> ids<-c("ENSG000000282326","ENSG000000008311","ENSG000000323881")
> 
>> hsdef <-
> getBM(attributes=c("ensembl_gene_id","ensembl_transcript_id","hgnc_symbo
> l"),filters="ensembl_gene_id",values=ids, mart=ensembl)
> 
>> hsdef
> 
> NULL
> 
> 
> Please let me know, am I doing something wrong?

The only thing you did wrong was to input three Ensembl IDs that don't 
exist - try entering them individually on Ensembl's website, and you 
will see that you get no returned value.

Best,

Jim


> 
>  
> 
> Best regards
> 
> Galina
> 
> PS
> 
>> sessionInfo()
> 
> R version 2.5.1 (2007-06-27) 
> 
> i386-pc-mingw32 
> 
>  
> 
> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623