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

Leila

ADD COMMENTlink modified 6 days ago by Michael Love19k • written 6 days ago by lkianmehr0
0
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:

https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

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

ADD COMMENTlink written 6 days ago by Michael Love19k
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