DESeq2 duplicate row.names

Hi everyone!

I am running DESeq2 on two tabular files that were generated from Cufflinks. I keep getting the following error:

Error in read.table(file = file, header = header, sep = sep, quote = quote, :
duplicate ‘row.names’ are not allowed
Calls: get_deseq_dataset … lapply -> lapply -> FUN -> read.delim -> read.table

However, I triple checked my row names (which are gene names) and removed all duplicates and continue to get this error.

Anyone have experience on this? Thank you!!

1 Like

Hello @mlim

This particular error is probably because the inputs have a header line but that option isn’t checked on the tool form.

But even with that fixed, you’ll still have problems. DESeq2 is not designed to work with Cufflinks results.

FAQ: Covers common DE analysis troubleshooting plus links to tutorials: Extended Help for Differential Expression Analysis Tools

For even more help (now or later), click on the “deseq2” tag added to your post to find related prior Q&A.