October 2024

Differential Gene Expression Analysis Workflow


Spoiler Alert: Plots we are going to make

Shrinkage

When counts are low the variance is high

Eg.

  • sample 1 = 2, sample 2 = 4 (large variance)

  • sample 1 = 90, sample 2 = 100 (small variance)

Makes those genes appear more significant than they really are on plots

So we need to shrink the logFCs.

ggplot2 library

  • Basic syntax for building a plot