Question

biomaRt is not working

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shenwei1376 • 0

@shenwei1376-14643

Last seen 6.5 years ago

Hi everyone,

The biomart package stopped working for today. I used the exact same code I run several weeks ago, but now it can not be executed. The attached is my code and error message:

> library("biomaRt")
> ensembl=useMart("ensembl", dataset="hsapiens_gene_ensembl")
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.

Then I tried load a different dataset, still did not work!

It will be really appreciated if anyone can help!

biomart • 2.9k views

ADD COMMENT • link 7.0 years ago shenwei1376 • 0

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shenwei1376 • 0

@shenwei1376-14643

Last seen 6.5 years ago

The method Mike offered worked perfectly for me! Thank you Mike!

ADD COMMENT • link 7.0 years ago shenwei1376 • 0

score 1 · Accepted Answer · 2017-12-16

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Mike Smith ★ 6.6k

@mike-smith

Last seen 7 hours ago

EMBL Heidelberg

Please try updating your version of biomaRt using BiocInstaller::biocLite('biomaRt'). You need at least version 2.43.1 to reliably use the new Ensembl 91

It's always helpful to include the output of sessionInfo() to show people what versions of packages & R you are using.

ADD COMMENT • link 7.0 years ago Mike Smith ★ 6.6k

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Hi Mike,

I still am getting this error above. When I use BiocInstaller::biocLite('biomaRt') it only updates to version 2.38.0. Any ideas on how to get to version 2.43.1?

Thanks for the help.

Dave

ADD REPLY • link 5.7 years ago knuppdav • 0

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Hi Mike,

I still am getting this error above. When I use BiocInstaller::biocLite('biomaRt') it only updates to version 2.38.0. Any ideas on how to get to version 2.43.1?

Thanks for the help.

Dave

ADD REPLY • link 5.7 years ago knuppdav • 0

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I think that was a typo, and should have read 2.34.1, and 2.38.0 should be fine.

Note that the BiocInstaller package has been deprecated now, and you should use BiocManager. The installation instructions on https://bioconductor.org/packages/biomaRt/ reflect this.

If the problem remains please start a new post and include both the error message and the output of sessionInfo() so we have some more details about your setup.

ADD REPLY • link 5.7 years ago Mike Smith ★ 6.6k