Question: Something wrong with the BioMart server
0
4 months ago by
Dan Liang0 wrote:

Hi,

I got an error when I tried to call genes suing bioMart.

genemart = useMart(biomart="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl");
Error in listMarts() : Unexpected format to the list of available marts.


Please check the following URL manually, and try ?listMarts for advice. http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt

Then I checked the link, it is the right list, so I think there is something wrong with the BioMart server. Hope this is the right way to report this error. Very appreciate it if you could fix it.

Thanks!

Dan

biomart • 354 views
modified 4 months ago by Mike Smith4.0k • written 4 months ago by Dan Liang0

Same thing here:

ensembl = useEnsembl(biomart="ensembl", dataset="hsapiens_gene_ensembl") Error in bmRequest(request = request, ssl.verifypeer = ssl.verifypeer, : Not Found (HTTP 404).

Same thing here:

ensembl = useEnsembl(biomart="ensembl", dataset="hsapiens_gene_ensembl") Error in bmRequest(request = request, ssl.verifypeer = ssl.verifypeer, : Not Found (HTTP 404).

Answer: Something wrong with the BioMart server
2
4 months ago by
Mike Smith4.0k
EMBL Heidelberg / de.NBI
Mike Smith4.0k wrote:

I currently get an error when I visit the main Ensembl site. You can try querying one of the mirrors e.g.

mart <- useEnsembl(biomart = "ensembl",
dataset = "hsapiens_gene_ensembl",
mirror = "useast")


Values for the mirror argument are: useast, uswest, asia