[BioC] Using older Annotations in GenomeGraph Library

[Steffen at stat.Berkeley.EDU]

Hi Philippe,

You can connect to Ensembl 54 which is ncbi36 by:

mart = useMart("ENSEMBL_MART_ENSEMBL", host="may2009.archive.ensembl.org",
dataset="hsapiens_gene_ensembl")

That should give you the annotation you want.

Cheers,
Steffen


> Hi all,
>
> I'm currently using the GenomeGraph library to visualise my data.
> However, I'm currently encountering the following problem:
>
> The data I want to visualise is from Human Genome Build 36.3. I'm also
> loading gene annotation information using makeGeneRegion, which itself
> imports data from ensembl. My problem of course is, that my own data is
> generated on Build 36.3 and the genome annotation is based on Build 37.1.
>
> So my first idea was to use a older version of biomart, by:
> mart <- useMart("ensembl_mart_49", archive=TRUE, dataset=
> "hsapiens_gene_ensembl")
>
> This is not working, as I get the error message:
>  Invalid attribute(s): ensembl_exon_id
>
> Does anybody have any other ideas to solve this problem? Or maybe
> someone knows how to generate my own annotation information?
>
> Any help would be appreciated,
>
>     Philippe
>
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