Figure 16.

Plot of a Golden Spike "Unanticipated Negative" with Fold Change = 3. We also find some "unanticipated negatives" - genes which should be differentially expressed based on a large initial fold change, but which in practice do not appear to be. In the Golden Spike experiment 153553_at has a log 2 fold change of 3, yet it ranks 7246, 10007, 6034 and 6049 (out of 14010 genes in the comparison) using median ANOVA (1-p), median signed ANOVA (1-p), RMA and PLM measures, respectively. This plot of the within-chip z-scores (control arrays are in red, spiked-in arrays in cyan) and the corresponding p-values for the gene support the conclusion that 153553_at is a not differentially expressed and therefore an unanticipated negative.