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  3. Differential Expression Analysis with limma in R

Exercise

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.

Instructions

100 XP

The ExpressionSet object eset with the doxorubicin data has been loaded in your workspace.

  • Combine the variables genotype (WT vs. Top2b null) and treatment (PBS vs. Dox) into a single factor variable.

  • Use model.matrix to create a design matrix with no intercept.