biomaRt getBM() problem
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dhondalay • 0
@dhondalay-7652
Last seen 6.5 years ago
United Kingdom

I am pretty new to biomaRt, but when I run the following code, I am getting an error.

 

library(biomaRt)

GOannotations <- getBM(attributes = c("ensembl_gene_id", "peptide", "interpro_description"),
                            filters = "hgnc_symbol",
                            values = c("C9orf142"),
                            mart = useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", verbose = TRUE))

 

Error in getBM(attributes = c("ensembl_gene_id", "peptide", "interpro_description"),  : 

  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 to the mailing list.

biomaRt getBM • 1.4k views
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Thomas Maurel ▴ 790
@thomas-maurel-5295
Last seen 11 weeks ago
United Kingdom
Hello, I believe the “peptide” attribute doesn’t exist in the Ensembl gene mart. If you are interested in the “Ensembl peptide id” (e.g: ENSPXXXXXXXXXXX) then you should use “ensembl_peptide_id” instead of “peptide” in your query: GOannotations <- getBM(attributes = c("ensembl_gene_id", "ensembl_peptide_id", "interpro_description"), filters = "hgnc_symbol", values = c("C9orf142"), mart = useMart(biomart = “ensembl", dataset = "hsapiens_gene_ensembl", verbose = TRUE)) head(GOannotations) ensembl_gene_id ensembl_peptide_id interpro_description 1 ENSG00000148362 ENSP00000360682 NA The following functions will give you the Ensembl gene mart filters and attributes list: 1) listFilters 2) listAttributes Hope this helps, Thomas > On 23 Apr 2015, at 09:58, dhondalay_krishan [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org <https: support.bioconductor.org=""/> > User dhondalay_krishan <https: support.bioconductor.org="" u="" 7652=""/> wrote Question: biomaRt getBM() problem <https: support.bioconductor.org="" p="" 66964=""/>: > > > I am pretty new to biomaRt, but when I run the following code, I am getting an error. > > > library(biomaRt) > > GOannotations <- getBM(attributes = c("ensembl_gene_id", "peptide", "interpro_description"), > filters = "hgnc_symbol", > values = c("C9orf142"), > mart = useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", verbose = TRUE)) > > > Error in getBM(attributes = c("ensembl_gene_id", "peptide", "interpro_description"), : > > 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 to the mailing list. > > > You may reply via email or visit biomaRt getBM() problem > -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom
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