In order to examine the effect of Log2 and VSN transformations on the detection rate of differentially phosphorylated peptides, we applied the performance evaluation procedure (Section 4.2) to generate 48 pairs of arrays, and for each performance measure, we conducted a Levene’s test (Table 1) and a paired T-test (Table 2) to determine whether there is a significant difference between means of that performance measure for Log2 and VSN. For all cases where the p-value in Levene’s test was less than the significance level (α=0.05), the hypotheses that the population variances are equal is rejected. Therefore, for all measures paired t-tests assuming unequal variances were performed. Table 2 illustrates the t-statistics and p-values from the paired t-tests. Moreover, it depicts the average value of each performance measure for the Log2 and VSN methods. In all cases the degrees of freedom for the t-statistic was 47. These results indicate that the accuracy, sensitivity, and precision performance measures were significantly higher for VSN than for Log2 transformation. This result is in accordance with other studies in transcriptional DNA microarrays that indicate superiority of VSN over Log2 [19,31].