Figure 2.

Effects of probe set algorithms on fold-change calculations. Shown is the same data set in Figure 1, now normalized to time 0, with the Y axis showing fold-change. The calculated fold change from day 0 (baseline) to peak transcript induction at time point 3.0 days varies considerably from algorithm to algorithm. For example, PCA algorithm shows a 90-fold induction compared to baseline, while RMA and dCHIP show only 2.5-fold induction.