[BioC] biomaRt question
sdurinck at ebi.ac.uk
Tue Aug 9 19:13:25 CEST 2005
Which version of biomaRt do you use?
You need 1.1.7 or above.
As a new version of Ensembl gets released about every 2 months, changes to
the Ensmart schema are possible. When their schema changes, we currently
have to update biomaRt as well.
You can download the latest biomaRt version from the developmental packages.
For Windows users note that the version available via the Bioconductor
website seems to lack behind on the Linux version. The latest Windows
version can also be found here:
I'm totally puzzled by biomaRt this afternoon. I've used it in the past
without problem, and today I can't seem to get any annotation to any
probeset... (see example below)
Is there something obvious I'm doing wrong?
PS: The probeset in the example is well annotated in Ensembl, I've
checked on the website.
>> mart = martConnect()
- Connected to: ensembl_mart_32 -
- Connected to: vega_mart_32 -
- Connected to: snp_mart_32 -
- Connected to: sequence_mart_32 -
>> getGene(id = "1415670_at", array = "mouse430_2", mart=mart)
An object of class "martTable"
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