GenomicFeatures: makeTxDbFromBiomart works for mouse but not for human
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23 months ago
johan.gson • 0

Hi,

I'm experiencing a problem with GenomicFeatures: My goal is to get the average transcript length for genes. I can run the following line:

txdbM = makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl", transcript_ids=NULL, circ_seqs=DEFAULT_CIRC_SEQS, filter=NULL, id_prefix="ensembl_", host="www.ensembl.org", port=80, taxonomyId=NA, miRBaseBuild=NA)


This works well, and I get the data I need. However, when I try for human data, with the following line

txdbH = makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", transcript_ids=NULL, circ_seqs=DEFAULT_CIRC_SEQS, filter=NULL, id_prefix="ensembl_", host="www.ensembl.org", port=80, taxonomyId=NA, miRBaseBuild=NA)


I get the following error:

Download and preprocess the 'transcripts' data frame ... 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


Could someone help me with this? I'm using the default parameters of the function?

genome GenomicFeatures • 773 views
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Please post this at Bioconductor support site as suggested in error message.