Hi, 

I have used Salmon to quantify some 126 samples using the mouse ensembl reference cDNA transcriptome. Then I tried to obtained 

abundance values using tximport as follows:

txi.salmon <- tximport(files, type = "salmon", tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM", ignoreTxVersion = F)

names(txi.salmon)
head(txi.salmon$counts)

###Create a matrix of abundance (a.k.a lengthScaledTPM) from the tximport object and import it as a text dataframe

cts <- txi.salmon$counts
abn <- txi.salmon$abundance
samples_rc <- data.frame(cts)
samples_tpm <- data.frame(abn)

This has worked without errors many times. 

Then I wanted to used these values with DESeq2, but I've gotten the following error: 

ddsTxi <- DESeqDataSetFromTximport(txi.salmon, colData = metadata, design = ~condition + day + strain + centre)
Error in `rownames<-`(`*tmp*`, value = colnames(countData)) : 
  duplicate rownames not allowed

This is the first time this occurs and I have no idea what may be wrong, since I have used the same step many times successfully. 

Now, I understand that this is complaining about repeated gene names in the rows, but this has never happened before. 

 Can you give me an idea of what may have gone wrong?

Thanks 

Please ignore this. I found the mistake. 

My metadata table had some repeated samples, after removing them everything worked just fine. 

Thanks!