[BioC] Agilent probenames and biomaRt

James W. MacDonald jmacdon at med.umich.edu
Mon Sep 13 20:53:22 CEST 2010

Hi Patrick,

On 9/12/2010 3:22 PM, De Boever Patrick wrote:
> Dear all,
> I'm working with Agilent 4X44 K human arrays. I have a vector with
> Agilent probenames that I would like to annotate with biomaRt. I use
> the following command:
> getBM(attributes = c("with_agilent_wholegenome",
> "entrezgene","wikigene_name","wikigene_description"), filters =
> "with_agilent_wholegenome", values = probesS, mart = ensembl)
> I get output, but although the vector probesS with my probe names
> only contains unique identifiers,  biomaRt returns me identifiers
> with some of the identifiers replicated and which get an annotation
> NA.
> It seems like that the database is redundant. Is this possible? If
> not, how can I avoid this problem.

The database isn't actually redundant, but it might appear to be so. 
Regardless, it's a simple operation to remove rows that have an NA in 
the second column, which will remove all your duplicates.


> Thank you for your support,
> Best regards,
> Patrick De Boever
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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