Figure 4.

Comparison of different post-summarization normalization strategies. ROC charts of Golden Spike data using a 2-sided and a 1-sided test of DE, and using three different post-summarization normalization strategies. For these charts only the equal spike-ins are used as true negatives, and all spike-ins with FC > 1 are used as true positives. We only show results for the FC DE detection method. The top row relates to data sets created without any post-summarization normalization. The middle row relates to data sets created using all probesets for the loess normalization. The bottom row relates to data sets created using only the equal spike-in probesets for the loess normalization. The left column shows probesets selected using a 2-sided test of DE. The right column shows probesets selected using a 1-sided test of up-regulation.