Design matrix for 3 groups
In the hypoxia experiment, stem cells were exposed to 3 different levels of oxygen: 1%, 5%, and 21%. To contrast the cellular function in these 3 different environments, use the group-means parametrization to specify a linear model with a coefficient for each level of oxygen.
This exercise is part of the course
Differential Expression Analysis with limma in R
Exercise instructions
The ExpressionSet object eset with the hypoxia data has been loaded in your workspace.
- Use
model.matrixto create a design matrix with no intercept. Recall that the variable of interest for this study (3 oxygen levels) is in the columnoxygenof the phenotype data frame.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Create design matrix with no intercept
design <- ___(~___ + ___, data = ___(eset))
# Count the number of samples modeled by each coefficient
colSums(design)