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CHAPTER 19. EXPRESSION ANALYSIS 386 Diamond Circle Triangle Reverse triangle Dot • Dot color. Allows you to choose between many different colors. Click the color box to select a color. Note that if you wish to use the same settings next time you open a box plot, you need to save the settings of the Side Panel (see section 5.6). Interpreting the box plot This section will show how to interpret a box plot through a few examples. First, if you look at figure 19.28, you can see a box plot for an experiment with 5 groups and 27 samples. Figure 19.28: Box plot for an experiment with 5 groups and 27 samples. None of the samples stand out as having distributions that are atypical: the boxes and whiskers ranges are about equally sized. The locations of the distributions however, differ some, and indicate that normalization may be required. Figure 19.29 shows a box plot for the same experiment after quantile normalization: the distributions have been brought into par. In figure 19.30 a box plot for a two group experiment with 5 samples in each group is shown. The distribution of values in the second sample from the left is quite different from those of other samples, and could indicate that the sample should not be used. 19.3.2 Hierarchical clustering of samples A hierarchical clustering of samples is a tree representation of their relative similarity. The tree structure is generated by 1. letting each feature be a cluster
