Figure 6

Distribution of p -values of a DNA-microarray experiment simulated by SIMAGE . Data for 2200 genes, in 6 slides with technical duplicates hybridized in dye-swaps, was simulated using the MolGen experiment profile (supplementary Table T1) with some changes: π_- = 1% and π₊ = 2%, μ_- = -2 and μ₊ = 2), σ _bg = 700, and s = 30 % × μ. The main graph shows the resulting ratios after normalization plotted versus the p-value. The graph was simplified by removing genes with ratios between 2/3 and 3/2. The 66 genes for which differential expressions were modeled are depicted by blue diamonds. The remaining genes are depicted in purple squares. The small graph on the right demonstrates the reversed p-value dependency on the average signal for the 66 differentially expressed genes modeled. The average signal was calculated for each of the 66 genes over the maximum of 12 normalized measurements. Normalization was performed using Lowess normalization and differential expression tests were performed with the non-Bayesian Cyber-T implementation of a variant of the t-test [3]. The Cyber-T test provides the p-values, which indicate the probability that a given ratio is not differential caused by chance. Genes with less than 8 measurements were excluded from these tests and assigned a p-value of 1, in order to be able to present these genes in the graph.