Design matrix
The doxorubicin experiment is a 2x2 factorial design, so you will need to create a combined variable to use in the group-means parametrization.
This exercise is part of the course
Differential Expression Analysis with limma in R
Exercise instructions
The ExpressionSet object eset with the doxorubicin data has been loaded in your workspace.
Combine the variables
genotype(WT vs. Top2b null) andtreatment(PBS vs. Dox) into a single factor variable.Use
model.matrixto create a design matrix with no intercept.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Create single variable
group <- with(___(eset), paste(___, ___, sep = "."))
group <- factor(group)
# Create design matrix with no intercept
design <- model.matrix(~___ + ___)
colnames(design) <- levels(group)
# Count the number of samples modeled by each coefficient
colSums(design)