Output of the Differential Expression for RNA-Seq tool

The Differential Expression for RNA-Seq tool produces different numbers and types of statistical comparison tracks depending on the settings of the Comparisons panel. Depending on the choice either a Wald test or a Likelihood Ratio test is used. For example, assume that we test a factor called `Tissue' with three groups: skin, liver, brain.

Note: Fold changes are calculated from the GLM, which corrects for differences in library size between the samples and the effects of confounding factors. It is therefore not possible to derive these fold changes from the original counts by simple algebraic calculations.