Figure 4.

Relative signal versus signal intensity. Deviation plots, log(x_i/v) versus log(v), much like the MA plots of Yang et al. [11] for the three replicate oligonucleotide arrays (from left to right) from HIV-infected samples. The top three plots show systematic deviations before normalization, and the bottom three show deviations after qspline normalization. Plots for prenormalized data show a comparison of curve fits for: log-intensity scaling (red); lowess (green); invariant set (magenta); and qspline normalizations (blue).