[BioC] attributes in GenomeGraphs

[Mark Robinson]

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

On 05/08/2008, at 1:04 PM, Amanda Miotto wrote:

>
> In regards to the library GenomeGraphs, when I try to define a Gene,  
> I get
> the following error. I am following the instructions from The  
> GenomeGraphs
> user’s guide by Steffen Durinck∗and James Bullard†. Where would  
> I be going
> wrong? Also, I am curious about the structure of gene, as I am  
> trying to
> replicate it with RMySQL, having set up a mysql identical to the  
> ensembl
> one. In the list listAttributes, ensembl_gene_id is in there.
> Thanks,
>
>
>> gene = new("Gene", id = "ENSG00000095203",type = "ensembl_gene_id",
> biomart = mart)
> Error in getBM(c("structure_gene_stable_id",
> "structure_transcript_stable_id",  :
>  Invalid attribute(s): structure_exon_stable_id,
> structure_exon_chrom_start, structure_exon_chrom_end,  
> structure_exon_rank
> Please use the function 'listAttributes' to get valid attribute names
>
> Amanda Miotto
> a.miotto at griffith.edu.au
>
> Software Engineer.
> Research Computing Services
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------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852