[BioMart Users] cant retreive information for Ensembl genes version 62

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[BioMart Users] cant retreive information for Ensembl genes version 62

Naharajan Lakshmanaperumal
Hello,

I was trying to retreive gene related information for zebra fish using the archive site "apr2011- Ensembl version 62". 
When I tried to connect to the archive site using R biomart package. I get the following error

> fish_mart <- useMart("ENSEMBL_MART_ENSEMBL", dataset ="drerio_gene_ensembl", host = "apr2011.archive.ensembl.org", path = "/biomart/martservice", archive = FALSE)
Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : 
  The given dataset:  drerio_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.

The datasets are missing for the Ensembl genes 62 version. 

Thanks in advance for your help,
Naharajan







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Re: [BioMart Users] cant retreive information for Ensembl genes version 62

Rhoda Kinsella
Hi Naharajan
There is an issue with the registry file which I will report to our web team and we will fix this as soon as possible. Basically, if you look here:


you will see that host="archive.ensembl.org" but this should be host="apr2011.archive.ensembl.org".
Apologies for any inconvenience caused. 
Regards
Rhoda

On 15 Jul 2011, at 12:37, Naharajan Lakshmanaperumal wrote:

Hello,

I was trying to retreive gene related information for zebra fish using the archive site "apr2011- Ensembl version 62". 
When I tried to connect to the archive site using R biomart package. I get the following error

> fish_mart <- useMart("ENSEMBL_MART_ENSEMBL", dataset ="drerio_gene_ensembl", host = "apr2011.archive.ensembl.org", path = "/biomart/martservice", archive = FALSE)
Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : 
  The given dataset:  drerio_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.

The datasets are missing for the Ensembl genes 62 version. 

Thanks in advance for your help,
Naharajan






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Users mailing list
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus, 
Hinxton
Cambridge CB10 1SD,
UK.


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