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Error: biomaRt has encountered an unknown server error. HTTP error code: 502(404) #85

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AndoYutaro opened this issue Aug 3, 2023 · 1 comment

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@AndoYutaro
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I run the following code and still get an error message.
Using other mirror sites does not work.
Please let me know how to deal with this error.

ensembl <- useMart("ensembl", host = "https://asia.ensembl.org/")
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "https://asia.ensembl.org")
mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = "https://asia.ensembl.org")
genes3 <- getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", values = rownames(counts)
                 , mart = mouse, attributesL = c("hgnc_symbol"), martL = human, uniqueRows=T)

@chiguashaonv
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I met the same question, when i run the following code, it reported a error as below:

human <- useMart("ensembl",dataset="hsapiens_gene_ensembl")    
mouse <- useMart("ensembl",dataset="mmusculus_gene_ensembl")    
#trans symbol from mouse to human    
lib1_gene_h <- getLDS(attributes = "mgi_symbol",filters="mgi_symbol",values=lib1_gene,mart=mouse,attributesL = "hgnc_symbol",martL=human,uniqueRows = TRUE)    
Error: biomaRt has encountered an unexpected server error.    
Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl)    

so i tried a mirror, but it repoted a new error:

human <- useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", mirror = "useast")
mouse <- useEnsembl(biomart = "ensembl", dataset = "mmusculus_gene_ensembl", mirror = "useast")
#trans symbol from mouse to human
lib1_gene_h <- getLDS(attributes = "mgi_symbol",filters="mgi_symbol",values=lib1_gene,mart=mouse,attributesL = "hgnc_symbol",martL=human,uniqueRows = TRUE)
Error: biomaRt has encountered an unknown server error. HTTP error code: 502
Please report this on the Bioconductor support site at https://support.bioconductor.org/
Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl)

how can i fix this problem? thank you!

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