Dear All,

I am getting the following error when trying to use biomaRt to match rsIDs to their associated genes: 

"Error in value[[3L]](cond): Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down."

Here is my code:

mart_snp <- useMart(biomart = "ENSEMBL_MART_SNP",dataset="hsapiens_snp")
snp_to_gene <- getBM(filters="snp_filter", attribute=c("refsnp_id","ensembl_gene_stable_id", "associated_gene","chr_name"), values=gabriel_data$rs, mart=mart_snp)

where gabriel_data is a data.frame, with the rs column containing rsIDs.

I have tried using a different host--i.e. changing the first line of my code to:

mart_snp <- useMart(biomart = "ENSEMBL_MART_SNP",dataset="hsapiens_snp", host="www.ensembl.org")

but this gives the same error.

Would really appreciate your help!  Thanks in advance.

Hello,

This error could indicate a server or internet connection glitch. Alternatively, it could also be that "gabriel_data$rs" used as a filter is just too large. In this case, I would advise to split up this dataset in smaller chunks and run one query at a time.

Hope this helps,

Best Regards,

Thomas