biomaRt package and Ensembl
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Wendy_tan ▴ 20
@wendy_tan-24321
Last seen 4.0 years ago

I was trying to use the R/Bioconductor package biomaRt. When I ran the "ensembl <- useMart("ensembl")" in RStudio, it showed "Ensembl site unresponsive, trying useast mirror Error in curl::curlfetchmemory(url, handle = handle) : Timeout was reached: [useast.ensembl.org:80] Connection timed out after 10014 milliseconds".

I wonder how to fix that? My sessioninfo is R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041)

Thank you for your kind help!

Ensembl site unresponsive • 2.3k views
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@james-w-macdonald-5106
Last seen 3 hours ago
United States

You should use useEnsembl rather than useMart for most queries with biomaRt.

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Thank you for your suggestion. I tried "ensembl <- useEnsembl("ensembl")", still had the similar error.

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