The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease

Quality control of the raw data and MA plots. (A) Box plot of the raw PM log₂ intensities for the 46,227 probes on each array, shown on log₂ scale. The majority of the log₂ intensities are low, and the interquartile range (IQR, which is the range of the box) is very narrow. (B) MA plot of the raw PM log₂ intensity data of the array c at day 4 vs. the array b at day 2. (C,D) MA plots of the PM log₂ intensity after RMA + quantile + RMA (C) or normexp + cyclic loess + RMA (D) normalization for the same arrays. In the MA plot, the y-axis represents the log₂ intensity ratio (M:) between the two arrays (day 4 to day 2). The x-axis represents the average log₂ intensity of the two arrays (A:). The colors represent the different types of probes.