Hi,

I want to perform a biomaRt query on my RNASeq dataset to match the ensembl version ID to the hgnc symbol (for approx 1300 genes).

library("biomaRt")
listMarts()
listEnsembl(verbose=TRUE)
ensembl = useEnsembl(biomart="ensembl", dataset = "hsapiens_gene_ensembl", mirror="uswest")
mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "uswest.ensembl.org"))
Gene_ID <- rownames(dds_RNASeq)
df <- read.csv("/Users/Results.csv")
df <- as.data.frame(df)
Symbol_list <- getBM(filters= "ensembl_gene_id_version", attributes= c("ensembl_gene_id_version","hgnc_symbol"),values=Gene_ID,mart = mart, uniqueRows = F)

I have noticed that the command 'ListMarts()' doesn't return a list but I also don't get an error message - is this a problem? The output from the final command in the script above is:

'Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery, : 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'

I tried adding ensemblRedirect to the 4th line of script:

listMarts()
listEnsembl(verbose=TRUE)
ensembl = useEnsembl(biomart="ensembl", dataset = "hsapiens_gene_ensembl", mirror="uswest")
mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "uswest.ensembl.org", ensemblRedirect = FALSE))
Gene_ID <- rownames(dds_RNASeq)
df <- read.csv("/Users/Results.csv")
df <- as.data.frame(df)
Symbol_list <- getBM(filters= "ensembl_gene_id_version", attributes= c("ensembl_gene_id_version","hgnc_symbol"),values=Gene_ID,mart = mart, uniqueRows = F)

and get this error message:

'Batch submitting query [==============================>------] 85% eta: 2sError in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery, : 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'

Any tips on how to proceed would be great. I've tried changing the host and also making sure the results cache is cleared without any success.

Thank you

If you google your error message, you will see it all over the place. Ensembl database are just flaky right now. You can try changing the mirror. You can also try splitting up your query into smaller chunks that might be more likely to run to completion.