Entering edit mode
7.5 years ago
elhamdallalbashi
▴
20
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 ?
Why can't you just use the ensembl identifiers as row names?
you mean I use ENST instead of gene name?because after meta analysis it is difficult to match name with ensemble Transcript ID.
You are fairly unspecific with regard to which type of analysis you are doing...
And you can still match transcript IDs with genes, at any stage in your analysis. So that's not a valid argument.
cross-posted in r-help. I would suggest go for gene level summarisation unless there is a need for transcript level for specific reasons.
it is not intentional.My friend and I got a little confused in posting question.