normalizeScaling: Normalization by scaling
In qPLEXanalyzer: Tools for qPLEX-RIME data analysis

Description Usage Arguments Details Value Examples

Performs scaling normalization on the peptide/protein intensities (median or mean)

1	normalizeScaling(MSnSetObj, scalingFunction = median, ProteinId = NULL)

`MSnSetObj`	MSnSet; an object of class MSnSet
`scalingFunction`	function; median or mean
`ProteinId`	character; protein Id

In this normalization method the central tendencies (mean or median) of the samples are aligned. The central tendency for each sample is computed and log transformed. A scaling factor is determined by subtracting from each central tendency the mean of all the central tendencies. The raw intensities are then divided by the scaling factor to get normalized intensities.

The intensities can also be normalized based on the peptide intensities of a selected protein. For this the argument "ProteinId" allows you to define the protein that will be used for scaling the intensities.

An object of class MSnSet (see MSnSet-class)

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 <- normalizeScaling(MSnSet_data, scalingFunction=median)