Error in Limma-voom Duplicate Row Error


I’m conducting an RNA-Seq analysis on galaxy and I’m trying to use limma-voom to identify differential gene expression. When I input both files, I get the following error:

Error in data.frame(sample = basename(filenamesIn), filename = filenamesIn, :
duplicate row.names: /galaxy-repl/main/files/033/345/dataset_33345502.dat
Execution halted
Does anyone know why I would get this error message? My previous data is an output from kallisto and there are two columns per file I input: the transcripts ID and the est_counts. The transcript IDs are a bit odd looking and they look like : ENST00000631435.1. Perhaps this is the problem. I’m unsure which headers limma-voom accepts. I’m relatively new to galaxy.and any suggestions would be helpful.

Thank you!

with my experience of this, you cant DEG with limma when using kallisto
try Deseq2 and in “choose of input data” select “TPM value” and then selet kallisto and put your GTF file then execute.

try this i hope it works