Inspect the results

Differential Expression Analysis with limma in R

John Blischak

Instructor

Inspect the results

# Create a Venn diagram
vennDiagram(results)

Differential Expression Analysis with limma in R

Histograms of p-values

  • limma function topTable

  • Specify contrast

    • coef = "dox_wt"
    • coef = "dox_top2b"
    • coef = "interaction"
hist(runif(10000))

Differential Expression Analysis with limma in R

Volcano plot

  • limma function volcanoplot

  • x-axis: log-fold change in expression between contrasted groups

  • y-axis: log odds of differential expression

  • Specify contrast, e.g. coef = "dox_wt"

Differential Expression Analysis with limma in R

Testing for KEGG enrichment

  • limma function kegga and topKEGG

  • Specify contrast, e.g. coef = "dox_wt"

  • Specify mouse species with species = "Mm"

    • Mm == Mus musculus
Differential Expression Analysis with limma in R

Let's practice!

Differential Expression Analysis with limma in R

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