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Yijing • 0@d0a8eb95
Last seen 7 days ago
I followed the biomaRt tutorial but encountered the server problem.
There is no problem with the useMart() function.
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") rat = useMart("ensembl", dataset = "rnorvegicus_gene_ensembl")
But when I use getLDS(), the problem occurred:
getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"), filters = "hgnc_symbol", values = "MIF", mart = human, attributesL = c("refseq_mrna","chromosome_name","start_position"), martL = rat) Error: biomaRt has encountered an unexpected server error. Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl)
Does anyone know how to solve this problem? Many thanks!
Always worth checking in the browser if BioMart is working.
Unfortunately, the BioMart LDS functionality have been flaky for a while now e.g. Problems with biomaRt's getLDS , biomaRt error unable to fix: need help troubleshooting , https://github.com/grimbough/biomaRt/issues/61 I have contacted the Ensembl Helpdesk to see if there has been any progress on this issue