FIG. 5.

Scatterplots of M values in the potato experiment for all genes using different normalization and background correction methods. Black spots denote genes showing evidence for differential expression in two different background correction and normalization method combinations: loess normalization without background correction versus loess normalization with background correction half (A) or vsn normalization without background correction (B). M values after vsn normalization with background correction half are shown in relation with M values after vsn normalization with no background correction—(C) and loess normalization with background correction half—(D). All other genes are plotted in gray. The gray line shows linear dependance between M values.