The null hypothesis for two-sample Kolmogorov-Smirnov test is that inter-array technical replicates produced by Algorithm 1 and the phosphorylated arrays produced by Algorithm 2 have the same distribution as the original (template) arrays. The p-values reported by the tests were greater than the significance level (0.05) in 46 of 48 cases for inter-array technical replicates, and in 41 of 48 cases for synthesized differentially phosphorylated arrays (see Tables S1–S3). Thus, in general the null hypothesis cannot be rejected.