In order to compare the effect of variance stabilization methods on specificity, sensitivity, precision, and accuracy, we use the following procedure:Procedure:  Performance evaluation
Input:  {A1,⋯,An} , a set of n actual kinome arrays
nd, the maximum number of differentially phosphorylated peptides on each pair of arrays
T, the threshold value for significant fold-change
θ, percentage of noisy peptides
α, a significance level
n′, number of synthesized arrays (n′≤n)
Output:  Calculated value of specificity, sensitivity, accuracy, and precision for each pair of inter-array technical replicates, and for each normalization method
Step 1:  For each q, where 1≤q≤n′, do Step 2 through Step 8:
Step 2:  Using Algorithm 1, create an inter-array technical replicate Yq, where Yq is an inter-array technical replicate for Aq, considering {A1,⋯,An}, T, θ and α.
Step 3:  Phosphorylate a random subset of peptides on Yq using Algorithm 2, considering {A1,⋯,An}, Aq, T, and α; exclude peptides that cannot be differentially phosphorylated by Algorithm 2 from the random subset and record the differentially phosphorylated peptides regardless of their fold-change direction in a set Pq; name the output as Yq′.
Step 4:  For each normalization method do steps 5 to 8.
Step 5:  Normalize the pair (Aq,Yq′), and denote the normalized array pair (Aq*,Yq*).
Step 6:  For the pair (Aq*,Yq*) detect the phosphorylated peptides and save them in a set Fq.
Step 7:  Calculate true positive (TPq), false positive (FPq), true negative (TNq), and false negative (FNq) sets as follows: TPq=Pq∩FqFPq=(Nq−Pq)∩FqTNq=(Nq−Pq)∩(Nq−Fq)FNq=(Pq)∩(Nq−Fq) where Nq is the set of all peptides on array Yq.
Step 8:  Using TPq, FPq, TNq, and FNq, calculate specificity, sensitivity, accuracy, and precision.