Quantile Normalization

This function is a wrapper around limma::normalizeQuantiles(). It normalizes the expression matrix by quantile normalization. This method is used to remove technical variation between samples. Proteomics data rarely uses this method, but it is common in microarray data. See wikipedia for more information.

Usage

normalize_quantile(x, by = NULL, ...)

Arguments

x

Either a glyexp_experiment object or a matrix. If a matrix, rows should be variables and columns should be samples.

by

Either a column name in sample_info (string) or a factor/vector specifying group assignments for each sample. Optional. If provided, the normalization will be performed within each group.

...

Additional arguments to pass to limma::normalizeQuantiles().

Value

Returns the same type as the input. If x is a glyexp_experiment, returns a glyexp_experiment with normalized expression matrix. If x is a matrix, returns a normalized matrix.