FIGURE 3.

The impact of robust estimation on normexp background correction. Box plots of log₂ (A) raw intensities, (B) normexp background corrected intensity, and (C) robust normexp background corrected intensity. All 46,227 probes were used in these plots. After normexp background correction (B), the variability between the arrays is smaller, as the IQR in each array is smaller. However, two arrays, day 3 array c and day 4 array a, have abnormal higher intensities for both miRNA and GC background control probes (here called negative control probes—“neg. controls”) following normexp background correction. This does not agree with the RT-qPCR results shown in Figure 1C, which showed very small variations between the biological replicates. These two arrays have the largest log-variance from normexp model parameter estimates, suggesting that “robust normexp” could resolve these variations. Using robust normexp, the log-variance was estimated to be smaller than ordinary normexp, and the background corrected log₂ intensities of each array were in similar ranges, with small IQR (C), indicating that robust normexp is more suitable than ordinary normexp.