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Figure 3shows the histogram and Figure 4the boxplot of correlations of θs estimated from the 20-probe difference model and θs estimated from the 10-probe difference model (a), the 20-probe PM-only model (b) and the 20-probe MM-only model (c).
If, for a probe set, a simplified model (PM-only, MM-only or 10-probe difference model) performs reasonably well, we expect its θ estimates to correlate with that from the 20-probe difference model.
The MM-only model yields noticeably lower correlations, however.
We fit a PM-only and an MM-only model to obtain expression values of all 20-probe probe sets using array set 1. For comparison, we also used half of the probe pairs (by alternatively picking one out of every two probes) in a 20-probe probe set to fit to the difference model (equation 1).