[R] Duplicate row.names of lncRNA

Vivek Das vd4mmind at gmail.com
Tue Nov 8 18:38:44 CET 2016

This is cross posted in Biostars https://www.biostars.org/p/221116/ . I do
not see any problem with duplicate row names unless you have specific
reasons to keep them. Here you are performing with transcript ids either
with refseq or ensemble. Now every gene does not have unique transcript
ids, they have alternative splicing events and more than one trascripts.
That is one main reason we perform gene summarisation. So you can go for a
gene level count matrix generation or expression value generation , then
this should be handled unless you want only transcript level output.

-- V.D

On Tue, Nov 8, 2016 at 6:01 PM, Elham - via R-help <r-help at r-project.org>

> I want to do meta analysis for lncRNA,but there is this error : Duplicate
> row.names are not allowedso some genes that are duplicate were detected,for
> example:PGM5-AS1-001 ENST00000417887.1PGM5-AS1-001 ENST00000613309.4when 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?
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