I have recently found that the following query (which used to work perfectly) is now failing:

library(biomaRt) ensembl = useMart( "ensembl", dataset = "hsapiensgeneensembl" ) genes <- c("ENSG00000121671", "ENSG00000142208", "ENSG00000171051", "ENSG00000115271", "ENSG00000143537") getBM(attributes=c('ensemblgeneid','entrezgene','hgncid','hgncsymbol'), filters='ensemblgeneid', values=genes, mart=ensembl) Error in getBM(attributes = c("ensemblgeneid", "entrezgene", "hgnc_id", : Invalid attribute(s): entrezgene Please use the function 'listAttributes' to get valid attribute names

The error is also happening in the package vignette: https://www.bioconductor.org/packages/devel/bioc/vignettes/biomaRt/inst/doc/biomaRt.html

affy=c("202763at","209310sat","207500at") select(mart, keys=affy, columns=c('affyhgu133plus2','entrezgene'), keytype='affyhgu133plus2') Error in getBM(attributes = columns, filters = keytype, values = keys, : Invalid attribute(s): entrezgene Please use the function 'listAttributes' to get valid attribute names

Is this a bug or has the functionality of getBM() changed in a recent update? Or has the 'entrezgene' field been removed?

Thanks!

The entrezgene attribute was changed to entrezgene_id when Ensembl 97 was released. It was a straightforward renaming, so nothing else should be affected.

Thanks for pointing out the broken example in the vignette. I thought I'd caught and updated all instances of this, but that one obviously slipped through.