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## Figure 3.
-log. MSQ_{10}(p-values) against MSQ_{between }where MSQ_{between }≤ 5_{between }was calculated based on the gene expression measured for the three sample groups analyzed,
namely untreated HaCaT cells after 2, 4, and 12 hours. Results of three exemplary
pre-processing methods of different quality are shown. bg_rma_log_loess exhibits the most unfavourable behaviour of the three. The p-values show a high variability
over the whole range of MSQ_{between }and even for small MSQ_{between }values there are many relatively high -log_{10}(p-values). Though for noBg_rankInvariant the p-values show less variability in general, especially for small MSQ_{between }values there are even more high -log_{10}(p-values). In contrast, noBg_log_rsn exhibits less varying p-values and does not assign as many small p-values to low
MSQ_{between }regions. The blue line represents a loess-curve fitted to the values. This curve takes
uniformly larger values for noBg_rankInvariant and noBg_log_rsn than for bg_rma_log_loess indicating, on average, smaller p-values for the same MSQ_{between }value. Thus, in Figure 1, quality values of -1, 0, and 2 are assigned to bg_rma_log_loess, noBg_rankInvariant, and noBg_log_rsn, respectively. For an overview of all different normalization methods and their quality
scores, see Additional file 1 and Figure 1.
Schmid |