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Thanks James -- Denise you can check the "note on factor levels" in the vignette.
And I'd recommend `plotCounts()` for looking at individu…
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As a trivial example, consider this:
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> model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4))))
(Intercept) Tre…
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The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
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