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  3. Differential Expression Analysis with limma in R

Exercise

Histogram of p-values

After performing the test, confirm that the model was properly specified by inspecting the distribution of p-values for each contrast. Recall that a uniform distribution of p-values is expected for a contrast with few differentially expressed genes, and a right skewed distribution is expected for a contrast with many differentially expressed genes.

Instructions

100 XP

The fitted model object fit2 has been loaded in your workspace. The limma package is already loaded.

  • Use topTable to obtain the summary statistics for every gene for the contrast "dox_wt". Set the number of genes to return equal the number of rows of fit2.

  • Repeat for the contrasts "dox_top2b" and "interaction".

  • Use hist to create a histogram of p-values for each of the three contrasts.