Normalization

Apply a specified type of normalization to the data.

Usage

normalize(dataSet, method = "quantile")

Arguments

dataSet

A data frame containing the data signals.

method

A string (default = "quant") specifying the method of normalization to apply:

1. Row-wise (sample-wise) normalization:

   • "mean": Samples are normalized to the mean value of all variables for a given sample.

   • "median": samples are normalized to the median value of all variables for a given sample.

   • "quantile": Quantile normalization.

2. Column-wise (metabolite-wise) normalization:

   • "meanCtr": Mean centering.

   • "medianCtr": Median centering.

   • "auto": Auto scaling.

   • "level": Level scaling.

   • "pareto": Pareto scaling.

   • "range": Range scaling.

   • "vast": Vast scaling.

Value

The normalized data.

Details

Quantile normalization is generally recommended. Mean and median normalization are going to be included as popular previous methods. No normalization is not recommended. Boxplots are also generated for before and after the normalization to give a visual indicator of the changes.