Median Normalization of Proteomics Data

Performs median normalization on the quantitative data within a ProtData object. This method corrects for systematic, sample-specific biases (e.g., differences in sample loading or instrument sensitivity) to make the samples more comparable.

The function operates by first calculating the median intensity for each sample (column). It then calculates the median of these medians (the "global median"). Finally, it scales the intensities in each sample by a multiplicative factor so that every sample has the same median abundance, equal to the global median.

Usage

median_normalize(object)

Arguments

object

A SummarizedExperiment object

Value

A SummarizedExperiment object with the abundance data in the assay slot normalized by the median-centering method.

Details

This type of multiplicative adjustment is typically appropriate for raw, non-log-transformed intensity data.