[BioC] question about biomaRt attributes

Elizabeth Purdom epurdom at stat.berkeley.edu
Wed Aug 20 08:06:57 CEST 2008


I am rerunning code I had using biomaRt. But I believe there is a change 
in the attributes. Before, everything was 'structure_xyz' from the 
Structure category:

anno <- getBM(c("structure_gene_stable_id",
                mart = mart)

Now it appears that it's just structure_transcript_stable_id, but the 
other attributes are under Gene or Exon, rather than Structure. I don't 
really know the distinction in this. Is it okay to mix these terms like 
I do here:

annoNew <- getBM(c("ensembl_gene_id",
                mart = mart)

I've run the code and don't see any obvious problems, but I would like 
to be sure -- it's hard to find out if there's a problem on just a tiny 
number of genes.

Thanks for any help,
UC, Berkeley

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