Figure 4. Evaluation of the minfi pipeline. (A) The difference in sample correlation (upper panel) or Euclidean distance (lower panel) between SWAN and raw data. For convenience, only samples represented by two or three technical replicates are shown. Color codes and positions of the samples are the same as Figure 2. (B) The absolute deviation between technical replicates in raw and SWAN-normalized data shows the reduction of the technical variability after normalization. (C and D) The logarithmic ratio between the variability after SWAN and the variability on raw data are shown for PB (C) and monocytes (D). For each probe, we calculated the average M-values and the corresponding mean absolute difference between technical replicates, as explained in Figure 2.