Question: DESeq Error: Duplicate rownames not allowed
0
gravatar for Yasavoli.h
7 weeks ago by
Yasavoli.h0
Yasavoli.h0 wrote:

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.

deseq2 • 60 views
ADD COMMENTlink modified 7 weeks ago by Michael Love23k • written 7 weeks ago by Yasavoli.h0
Answer: DESeq Error: Duplicate rownames not allowed
1
gravatar for Michael Love
7 weeks ago by
Michael Love23k
United States
Michael Love23k wrote:

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.

ADD COMMENTlink written 7 weeks ago by Michael Love23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 150 users visited in the last hour