Median Quotient Normalization

This approach is based on the calculation of the dilution factor of each sample with respect to a reference sample. Here, the reference sample was calculated as the median value of each glycan's abundance across all measured samples. For each sample, a vector of quotients was then obtained by dividing each glycan measure by the corresponding value in the reference sample. The median of these quotients was then used as the sample's dilution factor, and the original sample values were subsequently divided by that value. The underlying assumption is that the different intensities observed across individuals are imputable to different amounts of the biological material in the collected samples. See this paper for more information.

Usage

normalize_median_quotient(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.

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.