Question: biomaRt: Cannot access the zebra fish dataset
gravatar for francois
15 months ago by
francois10 wrote:

I cannot access the zebra fish ensembl database with biomaRt in R...

# biomaRt
library (biomaRt)


ensembl <- useMart("ensembl")

listDatasets(ensembl) #output is really bad, with huge spaces between lines (cannot copy it here)


Can't see the zebra fish dataset in the list!

ensembl = useDataset("drerio_gene_ensembl", mart = ensembl)

That returns:

Error in useDataset("drerio_gene_ensembl", mart = ensembl) : 
  The given dataset:  drerio_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.

While it looks like the correct name (I'm following a tutorial)... What is happening?

biomart R • 640 views
ADD COMMENTlink modified 15 months ago by Mike Smith1.1k • written 15 months ago by francois10
gravatar for Mike Smith
15 months ago by
Mike Smith1.1k
EMBL Heidelberg / de.NBI
Mike Smith1.1k wrote:

There was an issue with one of the new primate datasets having an apostrophe in its description, which was causing listDatasets() to fail. I have patched this in version 2.35.1 and pushed it to the Bioconductor devel branch. This will take a few days to propagate, so the fastest way to get hold if it is via Github using


If people could report back if that works or not that would be very helpful, and assuming it works I will also patch the release version of biomaRt.

> library(biomaRt)
> packageVersion("biomaRt")
[1] ‘2.35.1’

> ensembl_mart <- useMart("ensembl")
> dim( listDatasets(ensembl_mart) )
[1] 97  3
ADD COMMENTlink written 15 months ago by Mike Smith1.1k

Amazing, that works beautifully. I was stuck with 46 datasets for whatever reason, now I have all 97 available. Thanks Mike!

ADD REPLYlink written 15 months ago by francois10
gravatar for Sej Modha
15 months ago by
Sej Modha4.1k
Glasgow, UK
Sej Modha4.1k wrote:

This is reported on the support forum of the bioconductor by other users too. A workaround is also presented there:

ADD COMMENTlink modified 15 months ago • written 15 months ago by Sej Modha4.1k
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