Differential expression analysis

Differential Expression Analysis with limma in R

John Blischak

Instructor

Differential Expression Analysis with limma in R

Differential Expression Analysis with limma in R

Differential Expression Analysis with limma in R

Differential Expression Analysis with limma in R

Differential Expression Analysis with limma in R

What is the goal of a differential expression analysis?

  • Identify the genes that are associated with a phenotype of interest
  • Examples:
    • The response to a stimulus like a drug
    • Changes during development
    • The effect of a genetic mutation
Differential Expression Analysis with limma in R

Why differential expression?

  • Novelty

    • Are there additional genes of interest?

  • Context

    • Is the measurement for a given gene unique or common?

  • Systems

    • Which biological pathways are important?
Differential Expression Analysis with limma in R

Many steps to complete an experiment

  • Design study
  • Perform experiment
  • Collect data
  • Pre-process data
  • Explore data
  • Test data
  • Interpret results
  • Share results
Differential Expression Analysis with limma in R

Caveats

  • Measurements are relative, not absolute

  • Statistical methods cannot rescue a poorly designed study

Differential Expression Analysis with limma in R

Let's practice!

Differential Expression Analysis with limma in R

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