biomaRt::getBM can't parse attributes from plants.ensembl.org archive

[edoardobertolini]

Hi,

I'm using an old version of plans.ensembl.org to access the maize AGPv4 reference.

ensemblPlants = useMart(biomart="plants_mart",host="eg49-plants.ensembl.org") listDatasets(ensemblPlants) maize = useDataset("zmays_eg_gene", mart=ensemblPlants) filters=listFilters(maize) attributes=listAttributes(maize) attributes[1:20,] maize_annot=getBM(attributes= c("ensembl_gene_id", "description", "gene_biotype"), mart=maize)

but getBM gives me this error: > maize_annot=getBM(attributes= c("ensembl_gene_id", "description", "gene_biotype"), mart=maize) Error in .processResults(postRes, mart = mart, hostURLsep = 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

This doesn't happened if I use the current version of plants.ensembl.org:

ensemblPlants = useMart(biomart="plants_mart",host="plants.ensembl.org") listDatasets(ensemblPlants) maize = useDataset("zmays_eg_gene", mart=ensemblPlants) filters=listFilters(maize) attributes=listAttributes(maize) attributes[1:20,] maize_annot=getBM(attributes= c("ensembl_gene_id", "description", "gene_biotype"), mart=maize) head(maize_annot)

Does anybody know why? Any suggestions?

Thanks!

Edo