Duplicated Gene Symbol names after geneID conversion
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Entering edit mode
23 days ago
asumani ▴ 70

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?

geneID • 249 views
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Entering edit mode

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

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