Figure 6.

Effects of normalization on R/G ratios of dye-swapped arrays. MA plots for replicate arrays A and B showing log(R_A/G_A) (left column) log(R_B/G_B) (centre column) and dye-swap normalized log((R_AG_B)/(G_AR_B)) (right column). The top row shows standard dye-swap normalization of otherwise unnormalized data. The middle and bottom rows show scaled print-tip lowess and scaled print-tip qspline normalization of the individual arrays and the subsequent dye-swap averaging normalization.