Contrasts matrix for 3 groups
To identify the differentially expressed genes between each of the 3 levels of oxygen, you need to define 3 pairwise contrasts.
Den här övningen är en del av kursen
Differential Expression Analysis with limma in R
Övningsinstruktioner
The ExpressionSet object eset with the hypoxia data and the design matrix you just created (design) have been loaded in your workspace.
- Use
makeContraststo define the 3 pairwise contrasts. Remember to use the column names from the design matrix without using quotation marks.
Interaktiv övning med praktiskt arbete
Testa den här övningen genom att slutföra den här exempelkoden.
# Load package
library(limma)
# Create a contrasts matrix
cm <- makeContrasts(ox05vox01 = ___ - ___,
ox21vox01 = ___ - ___,
ox21vox05 = ___ - ___,
levels = design)
# View the contrasts matrix
cm