[ensembl-dev] Biomart connection

[Anne Lyle]

Hi Pankaj

Which database server are you connecting to? We are experiencing some network issues here in the UK, but if you’re connecting to the US East mirror I will need to look for possible server problems in the cloud.

Thanks

Anne


> On 18 Apr 2018, at 19:27, Pankaj Agarwal <p.agarwal at duke.edu> wrote:
> 
> Hi,
> I am trying to connect to biomart through R as follows and sometimes it works fine and sometimes I get the following error (today it only giving the error)
>  
> library("biomaRt")
> listMarts()
>                biomart               version
> 1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 92
> 2   ENSEMBL_MART_MOUSE      Mouse strains 92
> 3     ENSEMBL_MART_SNP  Ensembl Variation 92
> 4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 92
>  
> mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
> Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) :
>   The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.
>  
> This same command has worked several times in the past.
>  
> Thanks,
>  
> - Pankaj
>  
> ----------------------------------------------------------------
> Pankaj Agarwal, M.S
> Bioinformatician
> Database Analyst II
> Surgical Sciences Applied Therapeutics Section
> Department of Surgery
> Duke University
> 919-681-2251
> p.agarwal at duke.edu <mailto:p.agarwal at duke.edu>
>  
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Anne Lyle
www.ensembl.org
www.ensembl.info



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