Figure 6 and Figure 7 illustrate the effects of Log2 and VSN normalization, respectively, for the actual array and generated, differentially-phosphorylated replicate shown in Figure 5. In the scatter plots, the horizontal axis shows the actual array, while the vertical axis corresponds to the generated, differentially-phosphorylated replicate. The values on both axes were subjected to the transformation shown. In both figures the true differentially-phosphorylated peptides (set Pq of Step 3 in Section 4.2) are coloured in red to differentiate them from other peptides. Comparing Figure 6 and Figure 7 to Figure 5, it is obvious that Log2 destroys the information content for nonpositive average intensity values, while VSN preserves almost the same pattern as the raw array. However, VSN does not maintain fold-change values.