[ensembl-dev] R biomaRt : listDatasets issue

[Thomas Maurel]

Dear Mamun,

There was an issue with the biomaRt package and ensembl release 91 which would lead to the error you were seeing. Please see A: biomaRt: drerio_gene_ensembl dataset missing  <https://support.bioconductor.org/p/104025/#104043>or https://www.biostars.org/p/289654/#289861 <https://www.biostars.org/p/289654/#289861> for more details.

Updating your biomaRt package will fix the issue, more information here: https://www.bioconductor.org/install/#update-bioconductor-packages <https://www.bioconductor.org/install/#update-bioconductor-packages>

Hope this helps,
Kind Regards,
Thomas
> On 7 Aug 2018, at 15:58, rm8 <rm8 at sanger.ac.uk> wrote:
> 
> Hi All,
> I struggling to connect to ENSEMBL 93 using R biomaRt package. 
> listData set returns 68 datasets instead of 98 listed the example page and “hsapiens_gene_ensembl” is not included in the list. 
> 
> 
> > library("biomaRt")
> > listMarts()
> 
> ================
> 
> $               biomart               version
> 	1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 93
> 	2   ENSEMBL_MART_MOUSE      Mouse strains 93
> 	3     ENSEMBL_MART_SNP  Ensembl Variation 93
> 	4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 93
> 
> >  ensembl=useMart("ensembl")
> > dim(listDatasets(ensembl))
> 
> > dim(listDatasets(ensembl))
> 	[1] 68  3
>  	
> 
> > ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
> 
> 
> And when I try to connect using the dataset name I get the following error. 
> 
> $ Error in checkDataset(dataset = dataset, mart = mart) : 
>   The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
> 
>  
> Thanks in advance for help and suggestions. 
> 
> Mamun
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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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