Figure 4.

Normalization using composite normalization. MA-plots with a lowess normalization curve for the gene probes only (black), for the composite normalization (yellow) and for the MSP weighted lowess (red) with the MSP probes shown in blue. (a) The MSP probes do not extend to the full intensity range and the composite normalization curve follows the extension of the MSP only curve. (b) It can be seen that at low intensities the majority of gene probes are down-regulated compared to MSP probes, meaning that the lowess curve and, therefore, the composite normalization curve are biased downwards compared to the MSP.