RNA-Seq Data Analysis    ◾    209

type = ‘edger’,

padj = 0.05,

y.lim = NULL,

lfc = 2,

title = TRUE, legend = TRUE, grid = TRUE)

dev.off()

As shown in Figure 5.32, the blue points on the graph represent the genes with statistically

significant log-fold changes above the specified fold change indicated in the graph by the

dashed lines. The green points represent the genes with statistically significant log-fold

changes less than the specified fold change. The gray points represent the genes without sta-

tistically significant log-fold changes. Moreover, the values in parentheses for each ­legend

color show the number of genes that meet the conditions. The triangular shapes represent

values that are not displayed. The point size indicates the magnitude of the log-fold change.

5.3.8.4  Volcano Plots

As discussed above, the volcano plot is used to visualize the differential gene expression

between two conditions. The “vsVolcano()” function graphs -log10 of p-values in the y-axis

against the log2-fold changes in the x-axis (Figure 5.33).

jpeg(‘volcanoPlot2.jpg’)

vsVolcano(

x = ‘norm’, y = ‘tumo’,

data = yNorm,

d.factor = NULL,

type = ‘edger’,

padj = 0.05,

x.lim = NULL,

lfc = 2,

title = TRUE,

legend = TRUE, grid = TRUE,

data.return = FALSE)

dev.off()

5.4  SUMMARY

The PCR allows studying gene expression in very narrow scale since only expression of

few known genes can be investigated. Microarrays were emerged as the first technique for

studying the gene expression of massive number of genes. However, recently, the RNA-

Seq seems to replace microarrays because it is better at detecting gene transcripts and

gene isoforms and it also provides more accurate and sensitive results for differential gene

expression.

Studying gene expression allows researchers to identify the roles of genes in the biologi-

cal activities in the cells and their implications for diseases. This specifically provides broad

insight when massively parallel sequencing is used in the investigation of gene expression