Figure 3

Relative performance of the six methodologies for six summary contrasts of the data. MAS5, gcRMA, and dChip.mm consistently outperform the other methods, although all methods performed comparably on the 'Interaction' contrast. Correlations are lower for contrasts for which there is less differential expression, as seen in the scatterplots such as Figure 1 [see AdditionalFigures.doc]. However, the interesting comparisons are between the six correlations for a given contrast.