fferential expression/abundance.</p>
<p>We will use the CPTAC ovarian cancer proteomics dataset for this section. The required packages are MSnSet.utils for the LIMMA wrappers and volcano plots, dplyr for data frame manipulation, and ggplot2 for p-value histograms and to further customize the volcano plots. We load the <code>cptac_oca</code> data and copy <code>oca.set</code> to <code>m</code>, which will be used in the examples.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="so