Seem like the attribute corresponding filter "refseq_mrna" has got a different internal name in the Ensembl gene v64 (Human) configuration. that needs to be set to same name, and configurations made available again. Rhoda would know the time line of this.
Best, Syed ________________________________________ From: [email protected] [[email protected]] On Behalf Of Vincent Legagneux [[email protected]] Sent: Wednesday, September 28, 2011 7:22 AM To: [email protected] Subject: [BioMart Users] Error while using the RefSeq_mRNA filter in biomart 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] _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
