Gene-wise main and interaction effects of transcription levels for a two-factor model. Interaction plots for genes AT1G69530 (A) and AT1G61520 (B). The black lines represent the observed log2 expression for the probes at the different combinations of the two factor levels. The dotted grey line is corresponding the mean observed log2 expression over all the probes in the region. The orange lines are the probe-wise fitted log2 expression values, while the purple line gives the corresponding mean fitted log2 expression values for all the probes in the region.