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

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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 and dox_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

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