[BioC] help with biomart

[James W. MacDonald]

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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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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