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.
This exercise is part of the course
Differential Expression Analysis with limma in R
Exercise 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.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Load package
library(limma)
# Create a contrasts matrix
cm <- makeContrasts(ox05vox01 = ___ - ___,
ox21vox01 = ___ - ___,
ox21vox05 = ___ - ___,
levels = design)
# View the contrasts matrix
cm