Hi,

This code was working earlier today. Please help. Thanks.

R version 3.6.1 (2019-07-05) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 9 (stretch)

P.S.: My first question in this community

{r} ensembl <- useMart( "ensembl", "mmusculus_gene_ensembl" ) goi <- str_replace( NGdata2$Geneid, ".[0-9]+$", "" ) t_biomart <- getBM( attributes = c( "ensembl_gene_id", "external_gene_name", "gene_biotype" ), filters = "ensembl_gene_id", values = goi, mart = ensembl ) head(t_biomart)

Error in getBM(attributes = c("ensemblgeneid", "externalgenename", : 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

If the exact code was working earlier then in all likelihood it's fine. Ensembl are in the middle of transitioning to a new data centre (http://www.ensembl.info/2020/02/18/reduced-functionality-16th-25th-march-2020/) and there may be some reduced capacity for their services. I expect the pandemic and UK lockdown is not helping this go smoothly!

You could try querying one of the mirror sites, to see if it's more responsive.

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

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