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.

แบบฝึกหัดนี้เป็นส่วนหนึ่งของหลักสูตร

Differential Expression Analysis with limma in R

ดูคอร์ส

คำแนะนำการฝึกหัด

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 frame fit2$genes.
Create a volcano plot that highlights the top 5 genes for each of the 3 contrasts.

แบบฝึกหัดเชิงโต้ตอบแบบลงมือทำ

ลองทำแบบฝึกหัดนี้โดยเติมโค้ดตัวอย่างนี้ให้สมบูรณ์

# 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 = ___)

แก้ไขและรันโค้ด