DESeq2: Subset dataset or use interaction in design
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jeffsheng • 0
@jeffsheng-23603
Last seen 3.4 years ago

It is probably a statistics question rather than a question specific to the package. For example I have 2 cell lines A and B, each cell line has two conditions (treatment, control) If I want to access DEG for comparison treatment vs control in cell line A, which of the following approaches is preferred or they are equal?

#1. 
    ddsA = dds[dds$cell.line == "A"]
    design(ddsA) = formula(~condition) 
    dds = DESeq(ddsA) 
    results = results(dds, contrast = c("condition","treatment", "control"))

#2.
    dds$group <- factor(paste0(dds$cell.line, dds$condition))
    design(dds)= formula(~group) 
    dds = DESeq(dds) 
    results = results(dds, contrast = c("group","Atreatment","Acontrol"))
deseq2 • 1.3k views
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Entering edit mode
@mikelove
Last seen 1 hour ago
United States

This is actually covered by an FAQ in the vignette.

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Oh thanks Mike I see that part.

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