Contrasts matrix
To test for the effect of doxorubicin on the hearts of wild type and Top2b null mice (and any interaction between treatment and genotype), you need to contrast the coefficients from the design matrix.
This exercise is part of the course
Differential Expression Analysis with limma in R
Exercise instructions
The ExpressionSet object eset
with the doxorubicin data and the design matrix design
have been loaded in your workspace. The limma package is already loaded.
Create
dox_wt
to test the effect of doxorubicin in the wild type mice.Create
dox_top2b
to test the effect of doxorubicin in the Top2b null mice.Create an interaction term to test for differences in the response to doxorubicin between the two types of mice (hint: contrast
dox_top2b
anddox_wt
).
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Create a contrasts matrix
cm <- makeContrasts(dox_wt = ___ - ___,
dox_top2b = ___ - ___,
interaction = (___ - ___) - (___ - ___),
levels = design)
# View the contrasts matrix
cm