Figure 1.

Plot of mean log2 difference versus mean log2 intensity (MA plot) of C and S samples. MA plots for the (a) PM-only and (b) MAS5 PM-MM summary methods. Log2 differences greater than 0 imply that the average log2 intensity values in S samples are greater than C samples. Grey points represent empty probesets, black points represent FC = 1 probesets, and red points represent 'differentially expressed' FC > 1 probesets. The green 'x' is located at the mean log2 difference and mean log2 intensity of empty probesets.