DESeq uses the following model for differential expression analysis:
K_ij ~ NB(mu_ij, alpha_i)
mu_ij = s_j q_ij
log2(q_ij) = x_j. beta_i
Is there a way to access the specific 'mu_ij' and 'alpha_i' values?
I have been looking around and found assays(dds)[['mu']] giving something like mu_ij but am not sure if those are indeed the values that I am looking for.