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?