Deleted:biomaRt::getBM error for entrezgene_id (Ensembl version 107)
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@mgierlinski-7369
Last seen 3 months ago
United Kingdom

There is an error in biomart::getBM when one of the attributes is "entrezgene_id".

mart <- biomaRt::useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", version = 107)
biomaRt::getBM(attributes = c("entrezgene_id"), mart = mart)

returns the following error:

Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery,  : 
  Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'ensembl_mart_107.hsapiens_gene_ensembl__ox_entrezgene__dm' doesn't exist

The attribute in question exists:

attr <- biomaRt::listAttributes(mart)
grep("entrez", attr$name, value = TRUE)

which returns

[1] "entrezgene_trans_name"  "entrezgene_description" "entrezgene_accession"   "entrezgene_id"

It seems to affect only version 107. The same code for 106 and 108 works with no issues. I'm not sure if this is a problem with biomaRt of Ensembl.

biomaRt Ensembl • 468 views
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