Question: biomaRt is not working
0
gravatar for shenwei1376
16 months ago by
shenwei13760 wrote:

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 • 876 views
ADD COMMENTlink modified 16 months ago • written 16 months ago by shenwei13760
Answer: biomaRt is not working
1
gravatar for Mike Smith
16 months ago by
Mike Smith3.3k
EMBL Heidelberg / de.NBI
Mike Smith3.3k wrote:

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 COMMENTlink modified 16 months ago • written 16 months ago by Mike Smith3.3k

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 REPLYlink written 11 days ago by knuppdav0

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 REPLYlink written 11 days ago by knuppdav0

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 REPLYlink written 10 days ago by Mike Smith3.3k
Answer: biomaRt is not working
0
gravatar for shenwei1376
16 months ago by
shenwei13760 wrote:

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

ADD COMMENTlink written 16 months ago by shenwei13760
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