Within-Array Normalization. (A) rpd 3Δ probes plotted in the MA plane (ARS1 probes are indicated with green dots). (B) The background probe subset plotted in the MA plane. The first and second principal component axes are used as the new set of axes in the data rotation. (C) Probes plotted in a modified MA plane after data rotation. A loess curve is then fitted to the probes within two standard deviations of the median M-value. (D) Probes plotted in the modified MA plane after loess normalization is complete.