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  3. Differential Expression Analysis with limma in R

Exercise

Design matrix for group-means model

In the previous chapter, you tested the leukemia data for differential expression using the traditional treatment-contrasts parametrization. As a first step to learning the more flexible group-means parametrization, you will re-test the leukemia data to confirm you obtain the same results.

Instructions

100 XP

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

  • Use model.matrix to create a design matrix with no intercept. Recall that the variable of interest for this study (progressive vs. stable cancers) is in the column Disease of the phenotype data frame.