normalizeQuantiles: Quantile normalization

In crukci-bioinformatics/qPLEXanalyzer: Tools for quantitative proteomics data analysis

Quantile normalization

Description

Performs quantile normalization on the intensities within columns

Usage

normalizeQuantiles(MSnSetObj)

Arguments

MSnSetObj

MSnSet; an object of class MSnSet

Details

The peptide intensities are roughly replaced by the order statics on their abundance. This normalization technique has the effect of making the distributions of intensities from the different samples identical in terms of their statistical properties. It is the strongest normalization method and should be used carefully as it erases most of the difference between the samples.

Value

An object of class MSnSet (see MSnSet-class)

Examples

data(human_anno)
data(exp3_OHT_ESR1)
MSnSet_data <- convertToMSnset(exp3_OHT_ESR1$intensities_qPLEX1, 
                               metadata=exp3_OHT_ESR1$metadata_qPLEX1,
                               indExpData=c(7:16), 
                               Sequences=2, 
                               Accessions=6)
MSnset_norm <- normalizeQuantiles(MSnSet_data)

crukci-bioinformatics/qPLEXanalyzer documentation built on Oct. 23, 2023, 2:27 a.m.