thank you. this is bizarre... but now it works...
shouldn't this be fixed so that output of your query agrees with the input you have to provide for the query?






________________________________
From: James W. MacDonald <jmacdon@med.umich.edu>

Cc: bioconductor@stat.math.ethz.ch
Sent: Wed, 2 December, 2009 14:41:50
Subject: Re: [BioC] help with biomart

Hi Tereza,


Tereza Roca wrote:
> I found something wrong with biomart: if I request an illumina ID from an esembl gene ID I obtain the following: 
>> getBM(attributes = c("ensembl_gene_id","illumina_humanwg_6_v1"), filters="ensembl_gene_id", values = "ENSG00000165891", mart = ensembl)
>   ensembl_gene_id illumina_humanwg_6_v1
> 1 ENSG00000165891                    NA
> 2 ENSG00000165891               2350152
> 
> this is fine (altough why is there a NA?)
> 
> but if I request the contrary (from illumina to gene ID) I don't obtain anything:
> 
>> getBM(attributes = c("illumina_humanwg_6_v1","ensembl_gene_id"), filters="illumina_humanwg_6_v1", values = c("2350152"), mart = ensembl)
> [1] illumina_humanwg_6_v1 ensembl_gene_id      <0 rows> (or 0-length row.names)
> 
>  is this an error? or am I making some mistakes in the way I request it? Please advice

Well, you aren't doing the correct query, but I don't know if I would call it a mistake (or a weird 'feature' of how Illumina IDs are coded in the Biomart database). I figured this out by doing your first query at the Biomart server, which returned 0002350152 for the Illumina ID.

> getBM(attributes = c("illumina_humanwg_6_v1","ensembl_gene_id"), filters="illumina_humanwg_6_v1", "0002350152",mart)
  illumina_humanwg_6_v1 ensembl_gene_id
1               2350152 ENSG00000165891


Best,

Jim




> 
> thank you
> 
> Tereza
> 
> 
> 
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-- James W. MacDonald, M.S.
Biostatistician
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University of Michigan
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