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.
Cet exercice fait partie du cours
Differential Expression Analysis with limma in R
Instructions
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.
Exercice interactif pratique
Essayez cet exercice en complétant cet exemple de code.
# Load package
library(limma)
# Create a contrasts matrix
cm <- makeContrasts(ox05vox01 = ___ - ___,
ox21vox01 = ___ - ___,
ox21vox05 = ___ - ___,
levels = design)
# View the contrasts matrix
cm