quantro Additional Materials and Scripts
The additional materials (R code and scripts) for the paper When to use Quantile Normalization? authored by Stephanie C. Hicks and Rafael A. Irizarry are provided here.
quantro R/Bioconductor package is discussed in detail in the Supplementary Section 1 of the paper. This package contains a data-driven test for global differences between groups of distributions which asses whether global normalization methods such as quantile normalization should be applied.
quantroSim R package is discussed in detail in the Supplementary Section 3 of the paper. This is the supporting data simulation package for the
quantro R/Bioconductor package which can be used to simulate gene expression and DNA methylation data.
Applications to gene expression and DNA methylation
In this section, we apply
quantro to several gene expression and DNA methylation datasets. For a description of all the data used, see Table 1 in the Supplementary Material. Below are Rmarkdown files containing the analysis using
Gene expression (RNA-Seq)
Gene expression (Microarrays)
- Tumor/Normal examples
DNA methylation (Microarrays)
In this section, we perform several Monte Carlo simulation studies to assess the performance of our method in the
quantro R/Bioconductor package using the
quantroSim R-package (discussed in further detail in Supplementary Section 4).