Pre-process the data

Differential Expression Analysis with limma in R

John Blischak

Instructor

Mechanism of doxorubicin-induced cardiotoxicity

  • 2x2 design to study mechanism of doxorubicin:
    • 2 genotypes: wild type (wt), Top2b null (top2b)
    • 2 treatments: PBS (pbs), doxorubicin (dox)
    • Zhang et al. 2012
dim(eset)

Features  Samples 
   29532       12

table(pData(eset)[, c("genotype", "treatment")])

        treatment
genotype dox pbs
   top2b   3   3
   wt      3   3
Differential Expression Analysis with limma in R

Inspect the features

plotDensities(eset, 
    group = pData(eset)[, "genotype"], 
    legend = "topright")

Differential Expression Analysis with limma in R

Pre-processing steps

  • Log transform

  • Quantile normalize

  • Filter

Differential Expression Analysis with limma in R

Sanity check: Boxplot of Top2b

boxplot(<y-axis> ~ <x-axis>, main = "<title>")

boxplot(<gene expression> ~ <phenotype>, main = "<feature>")

boxplot(<Top2b expression> ~ <genotype>, main = "<Top2b info>")
Differential Expression Analysis with limma in R

Check sources of variation

  • Principal components analysis

  • limma function plotMDS

  • How many clusters do you anticipate?

Differential Expression Analysis with limma in R

Let's practice!

Differential Expression Analysis with limma in R

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