The hint is here:
duplicate 'row.names' are not allowed
rownames(data) should return a vector of only unique values, since it doesn't make sense to have the same gene/transcript in two different rows of your count matrix. How did you generate it?
which(duplicated(rownames(data))) return? Maybe that'll give you a hint on what went wrong. In general, if you use
kallisto for counting, you should use the excellent
tximport package to get the counts into R, then create a DESeq dataset with
The replies to my answer prompted me to re-read your post and I saw that you had set
tidy=TRUE, which means the duplicates are actually in your first column of your