Figure 1 shows an example result of applying Algorithm 1 for generating an inter-array replicate to an actual kinome array, “A-1”. In absence of noise, measurements for each peptide on inter-array replicates would be the same, and all points would lay on the identity line. However, this does not happen in the real world due to many sources of variability. Algorithm 1 allows the user to control the level of variability in generation of a synthesized kinome array using the fold-change threshold, percentage of noisy peptides, and significance level parameters (T, θ, and α, respectively). The result is shown in Figure 1 by points that deviate from the diagonal y=x. Figure 2 and Figure 3 show inter-array replicates for the same starting array with T = 3, θ = 0.10, and T = 4, θ = 0.15, respectively. In all three plots, the horizontal axis corresponds to the actual array, the vertical axis corresponds to the synthesized inter-array replicate, and each point depicts the average background-corrected intensity values for a peptide.