normalizeQuantiles {qPLEXanalyzer} | R Documentation

## 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)

[Package qPLEXanalyzer version 1.8.2 Index]