how to get ride of duplicated genes when we also have duplicated Ensemble ID in the expression profile?

how to get ride of duplicated genes when we also have duplicated Ensemble ID in the expression profile?

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Hi all,

I have a mouse expression profile that is annotated with gene symbols and many of them are duplicated. I usually use collapseRows function with maxMean method from WGCNA package to get ride of duplicated genes. However, this time I realized that there are also some duplication in ENSEMBLE IDs. Can any help me how should I deal with this situation?
Should I just simply remove duplicated ENSEMBLE ID and then use collapseRows function for duplicated genes?
This is part of my data:

ENSMUSG00000019864  Rtn4ip1 3.33471 2.18619 3.52304 4.13997 2.91682 3.17805
ENSMUSG00000019864  Rtn4ip1 0.141481    0   0.126809    0.140919    0   0.159667
ENSMUSG00000019865  Nmbr    0.0325972   0   0.056908    0.0324288   0.305734    0
ENSMUSG00000019866  Crybg1  8.79001 6.82754 13.9235 15.1803 9.54965 11.3725
ENSMUSG00000019867  Gje1    0   0   0   0   0   0

as you can see for example ENSMUSG00000019864 id is duplicated with different expression value?

I really appreciate any help or suggestion!


RNA-Seq


duplicated ENSEMBLE ID


collapseRows

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