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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