Hi,

Recently I have been getting an error with biomaRt that I didn't use to get with the same command.

The error is:

Batch submitting query [============================================================>---] 95% eta: 29sError in getBM(attributes = c("ensemblgeneid", "entrezgene", "hgnc_symbol"), : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this on the support site at http://support.bioconductor.org

Here is my code:

ensembl <- useMart("ensembl")
ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")    
mapping <- getBM(attributes = c("ensembl_gene_id", "entrezgene", "hgnc_symbol"), filters = "ensembl_gene_id", values = counts_table_annotated$`Ensembl ID`, mart = ensembl)

countstableannotated$Ensembl ID is a character vector of Ensembl IDs.

Any help with this error would be appreciated.

Best wishes, Lucy

To use one of the mirror sites you can do:

mart <- useEnsembl(biomart = "ensembl", 
                   dataset = "hsapiens_gene_ensembl", 
                   mirror = "useast")

Values for the mirror argument are: useast, uswest, asia.

This problem has been arising a lot recently, and I'm in contact with Ensembl to try and find a sustainable solution.