Duplicate genes with RSEM counts: Which one to choose? I have Ensembl ids in the first column and samples with RSEM counts data in other columns. I converted Ensembl ids to gene symbols. Now I see there are three genes repeated twice.

Gene   S1       S2       S3
COG8  804.07  1475.16  323.80
COG8  249.23   867.94  113.64
SDHD 1464.84  3508.02    75
SDHD  4.16     3.97       0
SOGA3 81.65   30.76    32.69
SOGA3 0.00    10.77    25.65


These are the Ensembl ids:


SOGA3: ENSG00000214338, ENSG00000255330
SDHD: ENSG00000204370, ENSG00000255292
COG8: ENSG00000213380, ENSG00000272617.


This is not for DE analysis, I want to do subtyping. Should I calculate mean or median on that? How should I go forward with this duplicate genes?
There is no one-to-one mapping of gene ids from one database to the other. Ensembl (who maintain Ensembl ENSG IDs), ncbi (who maintain EntrezGene IDs and RefSeq transcript ids) and HUGO (who maintain gene symbols/names) all have different ideas about what a gene is, which part of the genome belongs to which gene etc. 

In fact, it's worse than that because HUGO gene IDs refer to the abstract idea of a gene, rather than a particular part of any chromosome. 

My suggestion would be to leave the IDs as Ensembl IDs (as these actually refer to a physical part of a chromosome, which is what you are quantifying), right up until you have to report the results to someone who really NEEDS gene names. If you still have duplicates, you could sum, or pick the most interesting, but I would suggest just leaving the duplicates in there, and treat it as thought there are two genes with the same name.