Dear All,

Using R and BioMart, I get the following error message when trying to access the coding sequence of a gene:

mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

cds_seq = getSequence(id = "NM_004974", 
                      type = "refseq_mrna", 
                      seqType = "coding", 
                      mart = mart)

NULL Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery, : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this on the support site at http://support.bioconductor.org

Does anyone know what I can do to solve this problem?

Best, Heiko

Hey,

I believe Ensembl is doing some work in the background to move to a new data center. You can try again by simply switching the host / mirror, and then it should work:

require(biomaRt)

mart <- useMart('ensembl',
  dataset = 'hsapiens_gene_ensembl',
  host = 'uswest.ensembl.org')

cds_seq = getSequence(id = "NM_004974", 
  type = "refseq_mrna", 
  seqType = "coding", 
  mart = mart)

cds_seq
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        coding
1 ATGACAGTGGCCACCGGAGACCCAGCAGACGAGGCTGCTGCCCTCCCTGGGCACCCACAGGACACCTATGACCCAGAGGCAGACCACGAGTGCTGTGAGAGGGTGGTGATCAACATCTCAGGGCTGCGGTTTGAGACCCAGCTAAAGACCTTAGCCCAGTTTCCAGAGACCCTCTTAGGGGACCCAAAGAAACGAATGAGGTACTTTGACCCCCTCCGAAATGAGTACTTTTTCGATCGGAACCGCCCTAGCTTTGATGCCATTTTGTACTACTACCAGTCAGGGGGCCGATTGAGGCGACCTGTGAATGTGCCCTTAGATATATTCTCTGAAGAAATTCGGTTTTATGAGCTGGGAGAAGAAGCGATGGAGATGTTTCGGGAAGATGAAGGCTACATCAAGGAGGAAGAGCGTCCTCTGCCTGAAAATGAGTTTCAGAGACAAGTGTGGCTTCTCTTTGAATACCCAGAGAGCTCAGGGCCTGCCAGGATTATAGCTATTGTGTCTGTCATGGTGATTCTGATCTCAATTGTCAGCTTCTGTCTGGAAACATTGCCCATCTTCCGGGATGAGAATGAAGACATGCATGGTAGTGGGGTGACCTTCCACACCTATTCCAACAGCACCATCGGGTACCAGCAGTCCACTTCCTTCACAGACCCTTTCTTCATTGTAGAGACACTCTGCATCATCTGGTTCTCCTTTGAATTCTTGGTGAGGTTCTTTGCCTGTCCCAGCAAAGCCGGCTTCTTCACCAACATCATGAACATCATTGACATTGTGGCCATCATCCCCTACTTCATCACCCTGGGGACAGAGTTGGCTGAGAAGCCAGAGGACGCTCAGCAAGGCCAGCAGGCCATGTCACTGGCCATCCTCCGTGTCATCCGGTTGGTAAGAGTCTTTAGGATTTTCAAGTTGTCCAGACACTCCAAAGGTCTCCAGATTCTAGGTCAGACCCTCAAAGCCAGCATGAGAGAATTGGGCCTCCTGATATTCTTTCTCTTCATAGGGGTCATCCTTTTCTCTAGTGCTGTGTATTTTGCAGAGGCCGATGAGCGAGAGTCCCAGTTCCCCAGCATCCCAGATGCCTTCTGGTGGGCAGTCGTCTCCATGACAACTGTAGGCTATGGAGACATGGTTCCGACTACCATTGGGGGAAAGATAGTGGGTTCCCTATGTGCGATTGCAGGTGTGTTAACTATTGCCTTACCGGTCCCTGTCATTGTGTCCAATTTCAACTACTTCTACCACCGGGAGACAGAGGGAGAGGAACAGGCCCAATACTTGCAAGTGACAAGCTGTCCAAAGATCCCATCCTCCCCTGACCTAAAGAAAAGTAGAAGTGCCTCTACCATTAGTAAGTCTGATTACATGGAGATCCAGGAGGGTGTAAATAACAGTAATGAGGACTTTAGAGAGGAAAACTTGAAAACAGCCAACTGTACCTTGGCTAACACAAACTATGTGAATATTACCAAAATGTTAACTGATGTCTGA
  refseq_mrna
1   NM_004974

Kevin