Figure 1

Breakdown of lowess normalization. An MA-plot for a self-self hybridization is shown with a set of randomly selected genes designated to be differentially expressed at M = 2 or four-fold up-regulated. Results for 25% of genes on the array randomly being up-regulated are shown (a) before and (b) after print-tip lowess normalization. After normalization the fold change for most up-regulated genes has been reduced and bias has been introduced into the non-differentially expressed genes.