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grimbough / biomaRt

R package providing query functionality to BioMart instances like Ensembl
https://bioconductor.org/packages/biomaRt/
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Ensembl site unresponsive, trying useast mirror #70

Open Shicheng-Guo opened 1 year ago

Shicheng-Guo commented 1 year ago

Dear Team, How to handle this issue? Thanks. 

# from Human to Mouse
convertHumanGeneList <- function(x){

  library("biomaRt")
  human <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
  mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl")

  genesV2 <- getLDS(attributes = c("hgnc_symbol"), filters = "hgnc_symbol", 
                    values = x , mart = human, attributesL = c("mgi_symbol"), martL = mouse, uniqueRows=T)

  humanx <- unique(genesV2[, 2])

  return(humanx)
}

convertHumanGeneList("Tlx3")

convertHumanGeneList("Tlx3") Ensembl site unresponsive, trying useast mirror Ensembl site unresponsive, trying useast mirror Error: biomaRt has encountered an unexpected server error. Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl)

github-actions[bot] commented 1 year ago

Thank you for opening this issue.

Please note that the repository maintainer (@grimbough) is currently on parental leave until October 2022 and any response will take longer than usual.