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CHAPTER 3. EXPRESSION ANALYSIS
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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 ??).
Interpreting the box plot
This section will show how to interpret a box plot through a few examples.
First, if you look at figure 3.28, you can see a box plot for an experiment with 5 groups and 27
samples.
Figure 3.28: 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 3.29 shows a box plot for the same experiment
after quantile normalization: the distributions have been brought into par.
In figure 3.30 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.
3.3.2
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