Unable to convert GTEx v8 ensemble gene id+version to gene names using biomart
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22 months ago
pcmph ▴ 20

I am trying to convert GTEx v8 ensemble gene ids (+version) to gene names using biomart's archived ensembl version that corresponds to GTEx v8 (version 85). Example:

geneIDs=c("ENSG00000227232.5", ... ,"ENSG00000268903.1")

mart = useEnsembl(biomart="ensembl", dataset="hsapiens_gene_ensembl", version=85)

ensm=getBM(attributes=c("ensembl_gene_id", "external_gene_name"), filters = "ensembl_gene_id", values = geneIDs, uniqueRows=F, mart=mart)

I am getting no matches. I believe I need to use the attribute "ensembl_gene_id_version" but this option does not appear to exist in biomart's archived ensembl version 85 when checking here:

listAttributes(mart)

Any input would be much appreciated! Thank you.

biomart ensembl gtex • 657 views
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There is nice fix for this problem here, I know this is not perfect but seems thats the only way!!!

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