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  3. Differential Expression Analysis with limma in R

Exercise

Test for differential expression

Now that you have defined a design matrix and a contrasts matrix, you can test for differential expression due to doxorubicin treatment in the two types of mice.

Instructions

100 XP

The ExpressionSet object eset with the doxorubicin data, the design matrix design, and the contrasts matrix cm have been loaded in your workspace. The limma package is already loaded.

  • Fit the model coefficients with lmFit.

  • Fit the contrasts with contrasts.fit.

  • Calculate the t-statistics with eBayes.

  • Summarize the results with decideTests and vennDiagram.