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  3. Differential Expression Analysis with limma in R

Exercise

Gene ontology categories

In the previous exercise, you tested for enrichment of biological pathways. Now you will test for enrichment in gene sets that are known to influence the same biological process, known as gene ontology (GO) categories. Which GO categories are over-represented in the differentially expressed genes from the leukemia study?

Instructions

100 XP

The fitted model object of the leukemia study from Chapter 2, fit2, has been loaded in your workspace. The limma package is already loaded.

  • Extract the entrez Gene IDs from the data frame fit2$genes.

  • Test for enriched GO categories with goana. Set the species to "Hs" for Homo sapiens.

  • View the top 20 enriched GO categories with topGO. Set the argument ontology to "BP" to return Biological Processes.