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Question: biomaRt is not working
0
gravatar for shenwei1376
14 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 • 770 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by shenwei13760
Answer: biomaRt is not working
1
gravatar for Mike Smith
14 months ago by
Mike Smith3.2k
EMBL Heidelberg / de.NBI
Mike Smith3.2k 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 14 months ago • written 14 months ago by Mike Smith3.2k
Answer: biomaRt is not working
0
gravatar for shenwei1376
14 months ago by
shenwei13760 wrote:

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

ADD COMMENTlink written 14 months ago by shenwei13760
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