I want to convert ENSEMBL IDs to Gene Symbol. I use
select function from
org.Hs.eg.db package. The problem is I get duplicated Gene Symbol names after id conversion:
>countMatrix_GeneSymbol <- select(org.Hs.eg.db,countMatrix.log$geneID,"SYMBOL","ENSEMBL") 'select()' returned 1:many mapping between keys and columns >table(duplicated(countMatrix_GeneSymbol$SYMBOL)) FALSE TRUE 15721 3270
Duplicated IDs makes a trouble when I assign Gene Symbol names as rownames of my count matrix. One way to deal with duplicated names is to use
make.names function, but it doesn't sound like an optimal solution to me. How do you deal with this issue?