Figure 4

Comparisons of log ₂ fold changes detected with expired U133A and unexpired U133Plus2 microarrays (a) all 8,550 common genes; (b) the 6,835 genes with p < 0.05 in either expired U133A microarrays (2009) or unexpired U133Plus2 microarrays (2009); and (c) the 5,120 genes with p < 0.05 in both expired U133A (2009) and unexpired U133Plus2 (2009) microarrays. Fold changes were generated by comparing sample B to sample A, i.e., B/A. The blue and green dots indicated the up- and down-regulated genes, respectively. The red dots were the genes with reverse regulation directionalities. Under the three scenarios (a, b, and c), the overlap of differentially expressed genes between expired U133A (2009) and unexpired U133Plus2 (2009) microarrays is 89.94%, 96.99%, and 99.98%, respectively, indicating a high degree of consistency between differential gene expression data generated from expired U133A and unexpired U133Plus2 microarrays. Note that the fold changes measured with expired U133A microarrays exhibited some degree of compression (i.e., with smaller absolute values) when compared to those obtained with unexpired U133Plus2 microarrays.