[BioC] help with biomart

[Rhoda Kinsella]

Hi Tereza,
The Illumina ID that is returned to you via the bioconductor package  
has stripped three zeros from the front of the ID. If you carry out  
this search on the Ensembl mart interface you get:

Ensembl Gene ID  	Illumina HumanWG 6 v1
ENSG00000165891 	0002350152

If I then filter on ID 0002350152, I get the Ensembl gene ID in my  
result set. Can you re-try your query using the ID with the zeros and  
see if you get the correct result?
Regards
Rhoda


On 2 Dec 2009, at 14:15, 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
>
> thank you
>
> Tereza
>
>
>
>
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>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.