Figure 5.

Comparison of combinations of summarization/DE detection methods. ROC charts of Golden Spike data using a 2-sided and a 1-sided test of DE, using different combinations of summarization and DE detection methods. 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. A post-summarization loess normalization based on the equal-valued spike-ins was used. The different charts show a.) probesets selected using a 2-sided test of DE, and b.) probesets selected using a 1-sided test of up-regulation. The two legends refer to both a.) and b.)