When you have Fixed Effects for Differential Expression in your model, it is often of interest to compare differences among their levels using Volcano Plots. Specify the set of differences that you want to consider.
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All Pairwise Differences denotes differences between all possible pairs of levels.
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Simple Differences denotes all differences for which only one level has changed.
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Differences with a Control denotes taking differences against a single reference level. You can specify this level using the Control Levels for Differential Expression Comparisons option.
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Caution: All Pairwise Differences can generate numerous differences when there are many levels in your Fixed Effects for Differential Expression.
