Figure 1

MA-plots show, for two arrays, the average log intensity (x-axis) plotted against the log-ratio of intensities (y-axis). Here, we show the MA-plots for an array with spikes at concentration 3 pM against spikes at concentration 1 pM. In the top row, the arrays were transformed with a log₂ transformation or VST. In the bottom row, the arrays were background normalized before transformation. In all plots, red dots mark the values for the spike probes and the dotted lines indicate the predicted log fold-change of spikes (1.73) and non-spikes (0) respectively.