Section 5 Exploratory Data Analysis

Exploratory Data Analysis (EDA) is an important step before any sort of statistical analyses. The goal of EDA is to get a big picture view of the data and identify potential outlier samples and batch effects that need to be corrected. For this section, we need the MSnSet.utils package, which contains the cptac_oca data that we will use to illustrate these EDA approaches, as well as the plot_pca function for creating PCA plots of samples.

## Install missing packages
if (!require("remotes", quietly = T)) install.packages("remotes")
if (!require("MSnSet.utils", quietly = T))
  remotes::install_github("PNNL-Comp-Mass-Spec/MSnSet.utils")
## ------------------------
library(MSnSet.utils)

# Load the example MSnSet
data(cptac_oca)