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Em qui, 19 de abr de 2018 05:29, <dev-request at ensembl.org> escreveu:

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> Today's Topics:
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>    1. Biomart connection (Pankaj Agarwal)
>    2. Re: Biomart connection (Anne Lyle)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Wed, 18 Apr 2018 18:27:24 +0000
> From: Pankaj Agarwal <p.agarwal at duke.edu>
> To: "dev at ensembl.org" <dev at ensembl.org>
> Subject: [ensembl-dev] Biomart connection
> Message-ID:
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>
> 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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> ------------------------------
>
> Message: 2
> Date: Thu, 19 Apr 2018 09:29:04 +0100
> From: Anne Lyle <annelyle at ebi.ac.uk>
> To: Ensembl developers list <dev at ensembl.org>
> Subject: Re: [ensembl-dev] Biomart connection
> Message-ID: <2309E3AC-865F-4A13-B948-56CFBEA98279 at ebi.ac.uk>
> Content-Type: text/plain; charset="utf-8"
>
> 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
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