To recover the desirable symmetry between all levels, DESeq2 uses expanded design matrices, which include an indicator variable for each level of each factor, in addition to an intercept column (i.e., none of the levels is absorbed into the intercept). While such a design matrix no longer has full rank, a unique solution exists because the zero-centered prior distribution (see below) provides regularization. For dispersion estimation and for estimating the width of the LFC prior, standard design matrices are used.
