error in function useDataset of biomaRt
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Riley Qiu • 0
@71e7ea05
Last seen 6 weeks ago
China

Dear all, I am trying to use the biomaRt package to access the data from Ensembl, however I got error message when using the useDataset() function. My codes are shown below.

library(httr)
listMarts()
ensembl = useMart("ENSEMBL_MART_ENSEMBL")
listDatasets(ensemble)
ensembl = useDataset("hsapiens_gene_ensembl",mart = ensemble)


When I type useDataset function i got error message like this:

> ensembl1 <- useEnsembl(biomart = "ENSEMBL_MART_ENSEMBL",dataset = "hsapiens_gene_ensembl")
Ensembl site unresponsive, trying asia mirror
Error in textConnection(text, encoding = "UTF-8") :
invalid 'text' argument


and sometimes another different error message showed as:

> ensembl = useDataset("hsapiens_gene_ensembl",mart = ensembl)
Ensembl site unresponsive, trying asia mirror
Error in textConnection(bmResult) : invalid 'text' argument


it seems like that the mirror automatically change to asia OR useast OR uswest, but the error message still shows up over and over again, and i don't know what to do.

So if anyone could help me with this? I will be very grateful for any help or suggestion.

Kind regards Riley Qiu, Dongguan, China

bioma biomaRt • 132 views
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Try :

ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL",host="https://uswest.ensembl.org")
ensembl = useDataset("hsapiens_gene_ensembl",mart = ensembl)