[biomart-users] Problems with getBM function

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[biomart-users] Problems with getBM function

Claudia García Sánchez
Hi,
I'm running this code lines since two years ago:

mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = 'www.ensembl.org')
biotype <- biomaRt::getBM(attributes = c("gene_biotype", "external_gene_name", "description"), mart = mart)


But I've obtained this error today:

Error: failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no"


What can I do to fix it? Is there any problem with this URL?

Thanks.

Claudia

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Re: [biomart-users] Problems with getBM function

Steffen Durinck-2
Hi Claudia,

It seems that Ensembl changed their website's ability to be accessed by http and "broke" the biomaRt package.
This may lead to errors which look like this:

Details about this can be found at: https://support.bioconductor.org/p/134524/

I think a solution is to use the useEnsembl function instead of useMart or you could also install the dev version of biomaRt where this has been fixed.

Cheers,
Steffen

On Thu, Oct 15, 2020 at 6:08 AM Claudia García Sánchez <[hidden email]> wrote:
Hi,
I'm running this code lines since two years ago:

mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = 'www.ensembl.org')
biotype <- biomaRt::getBM(attributes = c("gene_biotype", "external_gene_name", "description"), mart = mart)


But I've obtained this error today:



What can I do to fix it? Is there any problem with this URL?

Thanks.

Claudia

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Re: [biomart-users] Problems with getBM function

Claudia García Sánchez
Thank you very much Steffen.

I will try using useEnsembl function.

Claudia

El jue., 15 oct. 2020 a las 17:53, Steffen Durinck (<[hidden email]>) escribió:
Hi Claudia,

It seems that Ensembl changed their website's ability to be accessed by http and "broke" the biomaRt package.
This may lead to errors which look like this:

Details about this can be found at: https://support.bioconductor.org/p/134524/

I think a solution is to use the useEnsembl function instead of useMart or you could also install the dev version of biomaRt where this has been fixed.

Cheers,
Steffen

On Thu, Oct 15, 2020 at 6:08 AM Claudia García Sánchez <[hidden email]> wrote:
Hi,
I'm running this code lines since two years ago:

mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = 'www.ensembl.org')
biotype <- biomaRt::getBM(attributes = c("gene_biotype", "external_gene_name", "description"), mart = mart)


But I've obtained this error today:



What can I do to fix it? Is there any problem with this URL?

Thanks.

Claudia

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Claudia García SánchezMSc Bioinformatics
Bioinformatics Scientist
C/ Finlandia, 2 1º
33010 Oviedo, Asturias (Spain)
+34 985 088 180



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