Figure 2

Comparisons of the log ₂ fold changes detected in 2009 and in 2005 using the same type of U133Plus2 microarrays (a) all 8,550 common genes; (b) the 7,069 genes with p < 0.05 in either 2009 or 2005; and (c) the 5,880 genes with p < 0.05 in both 2009 and 2005. 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 in 2009 and in 2005. Under the three scenarios (a, b, and c), the overlap of differentially expressed genes between 2009 and 2005 is 91.37%, 97.44%, and 99.78%, respectively, suggesting a high degree of stability of the two MAQC reference RNA samples.