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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: