Hello,

I am using biomaRt to match the probe IDs of microarray data with the associated gene symbol. I use ensembl as a database and the human gene set. To find the matching gene names, I use the function getBM and filter it with the probe IDs of my dataset.

ensembl <- useMart("ensembl") ensembl <- useDataset("hsapiensgeneensembl",mart=ensembl) affyid <- row.names(GSE41258) genenames <- getBM(attributes = c("affyhgu133a","hgncsymbol"), filters = "affyhgu133a",values = affyid, mart = ensembl)

I usually have no problem and already did it with several datasets. However, this time I get an error message :

Error in getBM(attributes = c("affyhgu133a", "hgncsymbol"), filters = "affyhg_u133a", : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.

I verify the plateform and its name in ensembl and it seems correct. I tried to run the code several times but no difference.

Can you help me ?

Thank you in advance,

Ysaline Bossicard

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