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  3. Differential Expression Analysis with limma in R

Exercise

Check sources of variation

Next you need to use principal components analysis to check for the sources of variation in the data. Do the samples cluster by their genotype (WT vs. Top2b null) and treatment (PBS vs. Dox)?

Instructions

100 XP

The ExpressionSet object eset with the doxorubicin data has been loaded in your workspace. The limma package is already loaded.

  • Use plotMDS to plot the principal components. Label the samples by their genotype.

  • Re-visualize the principal components, labeling the samples by their treatment.