Figure 3.

A) Responses, experiments and replicates form a nested group structure. B) These groups define a “similarity matrix”, a covariance matrix characterized by a block structure for Var X = Σ. The ${\sigma }_j^2$ marginal variances are given by Equation 8, ${\epsilon }_k=G_k^2+{\xi }_k$ is the within experiment covariance. G_k[jr] is the scaling factor for the experiment of the replicate corresponding to row j_r of the matrix, G_k[jc] is the same for column j_c.