4.1 DEA with limma

This section covers differential expression analysis with the limma package. The basic workflow for DEA with limma is to fit a linear model to each feature, then, empirical Bayesian methods are used to moderate the test statistics

The limma user’s guide is an invaluable resource.

4.1.1 Dichotomous Predictors

res1 <- limma_a_b(longitudinal_biomarker_study, 
                  model.str = "~ Type",
                  coef.str = "Type")

4.1.2 Continuous Predictors

4.1.3 Reference Level Comparisons

4.1.4 Custom Contrasts