Figure 1

Each source of variation included in the model is represented by a batch of parameters (see [15]). The batches, prior distributions and associated hyperpriors are given here. Parameters are indexed as follows: protein: i, peptide: j(i), treatment: c, experiment: q, tag (or channel): l, spectrum: t(q). For the normal distribution x ~ N(μ, τ), the form of the density is and for the gamma distribution τ ~ G(α, m), the form of the density is .