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  3. Differential Expression Analysis with limma in R

Exercise

Specify a linear model to compare 2 groups

To identify differentially expressed genes for the leukemia experiment, you need to translate the following linear model to R:

where \(X_{1}\) is equal to 1 for progressive cancers and 0 for stable cancers (note: R automatically chooses the base condition by alphabetical order).

Instructions

100 XP

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

  • Use model.matrix to construct a design matrix with an intercept coefficient and a coefficient that indicates the disease status.