biomaRt: Cannot access the zebra fish dataset

Question

[francois]

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

# biomaRt
library (biomaRt)

listMarts()

ensembl <- useMart("ensembl")

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

listDatasets(ensembl)$dataset

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?

[fatimarasool135]

Hi Mike Smith, I am using the biomart package. and i have not seen dataset of wheat. Can you please tell me how to acess the wheat dataset ?

[Mike Smith]

I would recommend you start a new topic with this question since it is unlikely to be the same issue as reported here, and include some details of the code you have already tried.

Answer 1

[Mike Smith]

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

BiocInstaller::biocLite('grimbough/biomaRt')

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

[francois]

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

Answer 2

[Sej Modha]

This is reported on the support forum of the bioconductor by other users too. A workaround is also presented there: https://support.bioconductor.org/p/104025/