DESeq2: correct way to extract comparison of comparisons
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adrtsc • 0
@b9ce134d
Last seen 3 days ago
Switzerland

Hi!

I am still quite new to DESeq2 and I would like to ask whether what I am doing is really what I WANT to do. My problem looks like this: I have two genotypes (I and II) and two conditions (A and B). I want to make a comparison of comparisons that should look like this:

(IIB vs IB) vs (IIA vs IA)

What I am doing currently is the following:


dds <- DESeqDataSetFromMatrix(countData = cts,
                              colData = coldata,
                              design =  ~genotype + condition + genotype:condition)
dds <- DESeq(dds)

res <- results(dds, contrast=list("genotypeII.conditionB", "genotype_II_vs_I"))

From what I was reading in the DEseq2 manual I assume that "genotypeII.conditionB" corresponds to the (IIB vs IB) comparison that I want to make and "genotype_II_vs_I" corresponds to (IIA vs IA). I would be very glad if someone could tell me if that is correct and if not maybe point me to the correct way to do it.

Thanks for the help!

DESeq2 • 129 views
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@mikelove
Last seen 1 hour ago
United States

Read the section on interactions. Ratios of ratios are defined by the interaction term alone.

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