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  3. Differential Expression Analysis with limma in R

Exercise

Test for differential expression for 2x2 factorial

Even though you have more contrasts than in the past examples, testing for differential expression with limma still uses the same pipeline.

Instructions

100 XP

The ExpressionSet object eset with the Populus 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.