Exercise

Revisiting PCA and Heat map

Now that you have identified the major differences between samples, you can create another set of plots to compare samples. These are very similar to the ones you looked at before, but this time you are only using differentially bound peaks. This reduces the amount of noise in the plot and helps to emphasize the differences. The DiffBind plotting functions have an argument contrast that allows you to specify which comparison should be used to select peaks for plotting. In this exercise, you will compare the original plots with their cleaned up counterparts.

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  • Create a PCA plot using all peaks.