[BioC] question about biomaRt attributes

Elizabeth Purdom epurdom at stat.berkeley.edu
Wed Aug 20 21:20:37 CEST 2008

Thanks Amanda for your response.

I guess I was not clear in my post. I did put the new attributes from 
listAttributes() in my code (I listed both my old code and my new code 
so it was clear what I had done and now what I was trying to do). I'm 
just not sure if I'm using the new attribute names correctly.

Previously I had to use special 'Structure' attributes to get the gene 
id, chromosome, etc. pulled down along with the transcript and exon 
information (or at least I thought I did). Now those attributes no 
longer exist. My new code assumes that now it just has a single 
identifier and there's no problem using the same 'ensembl_gene_id' 
attribute regardless of the category of other attributes are being 
pulled down with it. But I would like to know that this is correct 
because I am not comfortable with what these things mean and I don't 
want to have a hidden error somewhere.

Thanks a lot,

Amanda Miotto wrote:
> They upgraded. Have a look at the following posts:-
>> Amanda.
>> Have a look at Steffen's recent post:
>> https://stat.ethz.ch/pipermail/bioconductor/2008-August/023714.html
>> Basically, some internal changes to attribute names at biomart/
>> ensembl.  I think you have two options:
>> 1. Install the BioC 2.3 version of GenomeGraphs.
>> 2. Use 'listAttributes' (as the error message states) to get the
>> updated attribute names.
>> Cheers,
>> Mark
> Amanda Miotto
> a.miotto at griffith.edu.au
> Software Engineer.
> Research Computing Services
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