Current Analytical Methods of DNA Microarray Data - DNA Microarray Technology and Data Analysis in Cancer Research - page 30

Fig. 3.10. Histogram of the distribution of Fs permutation p -values resulting
from the contrast of RMA-processed data for sample groups Mut_A versus
B6 (top left), Mut_A versus Vector (top right), and Vector versus B6 (bottom
center).
3.3.4. Scatterplot of normalized intensities
A scatterplot of log 2 -transformed, quantile-normalized intensities
allows for the comparison of the degree of similarity (i.e. correlation)
of samples within a group to the degree of similarity of samples
between groups. Arrays are plotted in groups according to sample type
(Figs. 3.6 and 3.7).