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Error: biomaRt has encountered an unknown server error. HTTP error code: 404 #82

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hyjforesight opened this issue Jun 19, 2023 · 1 comment

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@hyjforesight
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hyjforesight commented Jun 19, 2023

Hello Biomart,
Thanks for developing this package.
I met HTTP error code: 404 when running below coding in China.

human <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl", mirror='asia')
mouse <- useEnsembl(biomart = "genes", dataset = "mmusculus_gene_ensembl", mirror='asia')
GeneMatrix=read.csv(file="C:/Users/hyjfo/Documents/mouse_var.csv", header = TRUE, sep = ",", quote = "\"")
mouse_gene <- GeneMatrix[,1]
human_gene <- getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", values = mouse_gene, mart = mouse, attributesL = c("hgnc_symbol"), martL = human, uniqueRows=TRUE)
Error: biomaRt has encountered an unknown server error. HTTP error code: 404
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)

Could you please help me with this?
Thanks!
Best,
Yuanjian

@hyjforesight
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hyjforesight commented Jun 22, 2023

I thought it could be the China connection issue. So, I asked my friend in Houston running below coding and met HTTP error code: 502

human <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl", mirror='useast')
mouse <- useEnsembl(biomart = "genes", dataset = "mmusculus_gene_ensembl", mirror='useast')
GeneMatrix=read.csv(file="C:/Users/hyjfo/Documents/mouse_var.csv", header = TRUE, sep = ",", quote = "\"")
mouse_gene <- GeneMatrix[,1]
human_gene <- getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", values = mouse_gene, mart = mouse, attributesL = c("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)

I also tried below coding, but doesn't work, either.

human <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl", host="https://dec2021.archive.ensembl.org/")
mouse <- useEnsembl(biomart = "genes", dataset = "mmusculus_gene_ensembl", host="https://dec2021.archive.ensembl.org/")
GeneMatrix=read.csv(file="C:/Users/hyjfo/Documents/mouse_var.csv", header = TRUE, sep = ",", quote = "\"")
mouse_gene <- GeneMatrix[,1]
human_gene <- getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", values = mouse_gene, mart = mouse, attributesL = c("hgnc_symbol"), martL = human, uniqueRows=TRUE)

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