Mapping of gene names in GSVA

Question

[mrashad]

Dears, I need to get the GSVA score using expression matrix and list of gene set. When trying to find out whether the genes in the expression matrix have the same nomenclature of genes in the gene set, I found that only 2 genes in the expression matrix have old nomenclature.

As follow: The expression matrix contains ATP5I instead of ATP5ME and ATPIF1 instead of ATP5IF1

What do you think, should I change them (2 genes) only into new nomenclature? or using BiomaRt and change the genes in the expression matrix and geneset into ensembl ids? Therefore the both inputs have the same base for gene nomenclature. or there is no difference between the 2 solution ?

Your opinions are appreciated