Question: how do compare with DESeq2
gravatar for lkianmehr
6 days ago by
lkianmehr0 wrote:

Hello to all,

I am starting to do DGE analysis with DESeq2 with a small example, as a first experiment I am going to compare two groups as example with DESeq2. I have two groups (ND and NF) and there 2 samples in each one (ND1 and ND2 in ND group, NF1 and NF2 in NF group). theses samples are COUNT file from HTseq-count. I am using this command in R for making groups, I am not sure they be correct;

gr <- factor(c(rep("ND", 2), rep("NF", 2)))
colData <- data.frame(group=gr, type="paired-end")
cds <- DESeqDataSetFromMatrix(cn2, colData, design= ~group)
cds <- DESeq(cds)
cnt <- log2(1+counts(cds, normalized=T))
dif <- data.frame(results(cds, c("group", "ND", "NF")))

I would be appreciate if would explain me they are right or not and how can I make group for DGE analysis

thanks in advance


ADD COMMENTlink modified 6 days ago by Michael Love19k • written 6 days ago by lkianmehr0
gravatar for Michael Love
6 days ago by
Michael Love19k
United States
Michael Love19k wrote:

This looks correct. Have you seen the DESeq2 workflow? This goes through the analysis at a slow pace to explain each step:

If you have further questions, feel free to post them.

ADD COMMENTlink written 6 days ago by Michael Love19k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 295 users visited in the last hour