Hello,
I was trying to recover Ensembl gene IDs from a list of RefSeq mRNA IDs
using the Biomart web interface (biomart.org). While retrieving the
results, I got this error message:
Serious Error: Error during query execution: Table
'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist ERROR: caught
BioMart::Exception::Database: Error during query execution: Table
'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist
A similar message was returned after having submitted the same query
through the Bioconductor biomaRt package:
library("biomaRt")
ensembl = useMart("ensembl")
ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
listFilters(ensembl)
data_ensg1=getBM(attributes = c("ensembl_gene_id"), filters =
"refseq_mrna", values = data[,4], mart = ensembl)
Error in getBM(attributes = c("ensembl_gene_id"), filters =
"refseq_mrna", :
Query ERROR: caught BioMart::Exception::Database: Error during query
execution: Table 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist
Does anybody have any clues on the origin of this error ?
Thanks a lot.
All the best,
vincent
Below are summarized the Biomart settings I used in the web interface:
Dataset
Homo sapiens genes (GRCh37.p5)
Homo sapiens genes (GRCh37.p5)
Filters
Refseq mRNA ID(s) [e.g. NM_001195597]: [ID-list specified]
Attributes
Ensembl Gene ID
Gene Start (bp)
Gene End (bp)
Strand
Chromosome Name
Associated Gene Name
Ensembl Gene ID
Ensembl Transcript ID
[2 enabled][2 enabled]
Ensembl Gene ID
Ensembl Transcript ID
[2 enabled][2 enabled]
Ensembl Gene ID
Ensembl Transcript ID
[2 enabled][2 enabled]
Ensembl Gene ID
Ensembl Transcript ID
Reference ID
[3 enabled][3 enabled]
Protein
Ensembl Gene ID
Ensembl Transcript ID
[3 enabled][3 enabled]
Dataset
[None Selected]
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