[R] Duplicate row.names of lncRNA

[Elham -]

I want to do meta analysis for lncRNA,but there is this error : Duplicate row.names are not allowed. 
so 35 genes that are duplicate were detected,for example:
PGM5-AS1-001 ENST00000417887.1      
PGM5-AS1-001 ENST00000613309.4     
when I search them in ensembl by its Transcript ID, one of them is antisense and another is lincRNA, with different bp. why?
for meta analysis,I should aggregate them as mean.is it true in this situation?
is it possible to change name of them by add 1,2.. for example: PGM5-AS1-001.1 and PGM5-AS1-001.2 ?
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