MA-plots for DE probes discovered by different normalization strategies (a) Tpl2 knockout vs wild-type at 180 mins and (b) Nfkb1 knockout vs wild-type at 180 mins. This figure highlights the log2 fold changes of DE probes discovered by different normalization strategies when comparing Tpl2-/- with wild-type at 180 mins and comparing Nfkb1-/- with wild-type at 180 mins. M-values (log2-fold-change between the two conditions) and A-values (average log2-intensity) were obtained from the linear models fitted to the probe intensities from strip-level normalization. Plots were generated using the plotMA function in the Bioconductor package limma. Probes in red, green and blue were discovered by strip-level normalization only, array-level normalization only, and both respectively. All other probes are in black. Numbers of DE probes can be found in Table 1.