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.

Take Hint (-30 XP)