Entering edit mode
Hello,
Has anyone else been getting inconsistent errors when using biomaRt with the hspaiens_gene_ensembl dataset?
for example:
mart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl")
will give the following error
Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets function.
However, if i repeatedly enter that line of code it eventually works, maybe after 3 or 4 tries? Does anyone else have any experience with this issue?
Sorry I didn't see this earlier. Are you still experiencing the issues? If so, can you update your post with the output of
sessionInfo()
so I can see which versions of R and biomaRt you're using.Sounds like you're experiencing the issue described in biomaRt: drerio_gene_ensembl dataset missing
This was caused by the Ensembl release at that time including some species with apostrophes in their name for the first time, which broke
listDatasets().
I suggest updating your version of biomaRt to at least 2.34.1 where a patch was introduced. You can do this via: