Entering edit mode
Hi, I'm getting this error:
Error in getBM(attributes = c(micrTypeFilter, "ensembl_gene_id"), filters = micrTypeFilter, : 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
when I do this:
micrTypeFilter <- "illumina_humanht_12_v4"
dataset <- "hsapiens_gene_ensembl"
ensembl = useMart(biomart ="ENSEMBL_MART_ENSEMBL", dataset = dataset)
ConversionTable <- getBM(attributes=c(micrTypeFilter,'ensembl_gene_id'),filters = micrTypeFilter, values = list(ids) ,mart = ensembl)
doing head(ids)
gives this:
[1] "ILMN_1343291" "ILMN_1343295" "ILMN_1651199" "ILMN_1651209" "ILMN_1651210" "ILMN_1651221"
What am I doing wrong?
This is certainly how
values
is intended to be provided, but I think biomaRt will simply unlist thevalues
in this case and it should still work.More likely switching to using the the US mirror avoids a timeout with the main site. I would recommend following James' example and defining the
mart
object via: