Duplicated Gene Symbol names after geneID conversion

Question

[asumani]

Hi all,

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?

Answer 1

[GenoMax]

See: How to deal with the case that one gene symbol matches multiple ensembl ids?

[asumani]

opss, didn't notice that thread. many thanks!