Question

biomaRt expected a character string of length 1

0

Entering edit mode

salamandra ▴ 20

@salamandra-12825

Last seen 2.3 years ago

Portugal

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?

biomaRt • 700 views

ADD COMMENT • link updated 4.5 years ago by James W. MacDonald 65k • written 4.5 years ago by salamandra ▴ 20

score 1 · Answer 1 · 2019-11-21

1

Entering edit mode

James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 1 day ago

United States

The values argument should be a character vector, not a list.

> library(biomaRt)
> mart <- useEnsembl("ensembl","hsapiens_gene_ensembl", mirror = "useast")
> getBM(c("illumina_humanht_12_v4","ensembl_gene_id"), "illumina_humanht_12_v4", c("ILMN_1343291", "ILMN_1343295", "ILMN_1651199", "ILMN_1651209", "ILMN_1651210", "ILMN_1651221"), mart)
  illumina_humanht_12_v4 ensembl_gene_id
1           ILMN_1651210 ENSG00000112679
2           ILMN_1343295 ENSG00000111640
3           ILMN_1343291 ENSG00000196205
4           ILMN_1343291 ENSG00000156508
5           ILMN_1343291 ENSG00000233476
6           ILMN_1651209 ENSG00000215790

ADD COMMENT • link 4.5 years ago James W. MacDonald 65k

1

Entering edit mode

This is certainly how values is intended to be provided, but I think biomaRt will simply unlist the values 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:

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

ADD REPLY • link 4.5 years ago Mike Smith ★ 6.5k