Volcano plot
Now you will visualize the extent of differential expression for each contrast with a volcano plot, which displays the log odds of differential expression on the y-axis versus the log fold change on the x-axis.
This exercise is part of the course
Differential Expression Analysis with limma in R
Exercise instructions
The fitted model object fit2 has been loaded in your workspace. The limma package is already loaded.
Access the gene symbols (
symbol) from the data framefit2$genes.Create a volcano plot that highlights the top 5 genes for each of the 3 contrasts.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Extract the gene symbols
gene_symbols <- fit2$genes[___]
# Create a volcano plot for the contrast dox_wt
___(fit2, coef = ___, highlight = 5, names = gene_symbols)
# Create a volcano plot for the contrast dox_top2b
___(fit2, coef = ___, highlight = ___, names = gene_symbols)
# Create a volcano plot for the contrast interaction
___(fit2, coef = ___, highlight = ___, names = ___)