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Question: biomaRt - rice genes database not working
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gravatar for maialiaeb
2.1 years ago by
maialiaeb0
maialiaeb0 wrote:

Hello! 

I'm having a problem with the rice genes database.

I'm using Package biomaRt version 2.30.0

R 3.3.1

> source("https://bioconductor.org/biocLite.R")
> biocLite("biomaRt")

> library(biomaRt)
> listMarts()

               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 86
2   ENSEMBL_MART_MOUSE      Mouse strains 86
3     ENSEMBL_MART_SNP  Ensembl Variation 86
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 86
5    ENSEMBL_MART_VEGA               Vega 66
 

And when I use:

> gramene = useMart('ENSEMBL_MART_ENSEMBL')

> listDatasets(gramene)

I don't get any of the gramene datasets.

Maybe I got a version problem, not sure. 

Thanks for the help

Kind regards,

Maia 

ADD COMMENTlink modified 2.1 years ago by Thomas Maurel770 • written 2.1 years ago by maialiaeb0
1
gravatar for Thomas Maurel
2.1 years ago by
Thomas Maurel770
United Kingdom
Thomas Maurel770 wrote:

Dear Maia,

You will need to connect to the Ensembl plants marts to be able to query Rice:

> listMarts(host="plants.ensembl.org")
            biomart              version
1       plants_mart           Plant Mart
2 plants_variations Plant Variation Mart

> gramene = useMart("plants_mart", dataset="osativa_eg_gene", host="plants.ensembl.org")

Hope this helps,

Regards,

Thomas

ADD COMMENTlink written 2.1 years ago by Thomas Maurel770

Thank you! It seems to work.

Now I have to learn how to do the query.

Thanks a lot for your help.

Regards, 

Maia 

 

ADD REPLYlink written 2.1 years ago by maialiaeb0
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