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  3. Differential Expression Analysis with limma in R

Exercise

Test for differential expression for 3 groups

Now that you've specified the design matrix and the contrasts matrix, you can test for differential expression.

Instructions

100 XP

The ExpressionSet object eset with the hypoxia data, the design matrix (design), and the contrasts matrix (cm) have been loaded in your workspace.

  • Fit the model coefficients with lmFit.

  • Fit the contrasts with contrasts.fit.

  • Calculate the t-statistics with eBayes.

  • Summarize the results with decideTests.