206    ◾    Bioinformatics

5.3.8.1  Visualizing Distribution with Boxplots

We can use “vsBoxPlot()” function to create box plots to study the distribution of the count

data based on condition studied. The count data can be FPKM or CPM normalized values.

The function uses the DGEList object and creates boxplots for the log10 of either FPKM or

CPM (Figure 5.30).

#Creating box plot

jpeg(‘boxplot.jpg’)

vsBoxPlot(

data = yNorm,

d.factor = NULL,

type = ‘edger’,

title = “Box plots of normal and tumor count data”,

legend = TRUE, grid = TRUE)

FIGURE 5.31  A scatter plot showing comparisons of log10 values of CPM for the two conditions.