[BioC] attributes in GenomeGraphs

[steffen at stat.Berkeley.EDU]

Hi Amanda,

This is now also fixed in the release branch.

http://bioconductor.org/packages/2.2/bioc/html/GenomeGraphs.html

or update with biocLite script.

Cheers,
Steffen


> 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
>> INFORMATION SERVICES
>> Griffith University, NATHAN 4111, AUSTRALIA
>> Phone:  +61 7 37354419  Fax:  +61 7 37356650
>> Web:    http://eResearch.griffith.edu.au/
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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
>
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