Figure 4

MA plots showing differences between Classic and refRMA models for the same test set. Mean probe set intensities as summarized by the two different RMA models are shown for the same test set of 15 normal liver samples. In each case, the y-axis (i.e., the axis indicating variability) is scaled relative to the biological variability observed in Figure 3 in order to contextualize the effect of model relative to effect of inherent variability contributed by different test set sampling. a) Classic and refRMA models differ somewhat, while b) the Full refRMA model and a refRMA model where liver has not been used in the training set are almost identical, indicating that the Full refRMA model is unaffected by incorporation of other single organs. For each probe set, the mean was calculated by averaging individual expression values across the 15 samples in each set.