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jeffsheng
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@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"))
Oh thanks Mike I see that part.