FIG. 3.

Scatterplots of M values in the potato experiment using different normalization and background correction methods. Plots depict M values obtained after loess normalization without background correction compared with the M values obtained for the same spots after loess normalization with the background correction method half (A) or vsn normalization without background correction (B). M values after vsn normalization with background correction half are shown in relation to M values after vsn normalization with no background correction (plot C) and loess normalization with background correction half (plot D). Spots that were flagged after preprocessing are shown in gray. The gray line shows linear dependence between M values. Correlations between all spots that were weighted with 1 (and thus kept for further analysis) were in all cases >0.96.