Hi I am Hamed. I have seen several answers for my problem with DESeq package; however, the solutions did work for me and I really appreciate it if you could help me. I am going to analyze R-seq. data consist of tumor and normal samples. The following is my codes:

cnt <- data colnames(cnt) <- c(rep("normal",31), rep("tumor",13)) gr <- colnames(cnt) colData <- data.frame(group=factor(gr), libType="single-end") cds <- DESeqDataSetFromMatrix(cnt, colData, design=~group)

here I have faced an error: Duplicate rownames not allowed.

I found that the problem is not with the rownames, itis the culnames. so, I choose a unique name for each columns (normal01, normal02, ..... or tumor01, tumor_02, ....) and the codes worked very well. once again, I faced another problem when I want to get differentially expressed genes using the following code:

res <- results(cds, c("group", "tumor", "normal"))

I have no idea how can I fix these problems. I was wondering if you could help me and show me a way to cope with these problems. Thank you for your time. All the best.

I think you can solve this by simply not putting column names on the counts matrix or rownames on the colData table.

colData should be a data frame with a factor variable as a column, with two levels “tumor” or “normal”, for your design.