In MassDynamics/MassExpression: MassExpression

print(params)
knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE, 
                      fig.path = params$output_figure, dev = "svg")

library(dplyr)
library(stringr)
library(MassExpression)
library(plotly)

CompleteIntensityExperiment <- params$listInt$CompleteIntensityExperiment
IntensityExperiment <- params$listInt$IntensityExperiment
design <- colData(IntensityExperiment)

comparisonExperiments <- 
    listComparisonExperiments(CompleteIntensityExperiment)

plot_rle_boxplot(IntensityExperiment, 
                 includeImputed = FALSE, 
                 plotRawRLE = TRUE, 
                 title = "RLE plot of initial log2(intensities)",
                 format = "html")