rowScaling: Normalization by scaling peptide/protein intensity across all...

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

Normalization by scaling peptide/protein intensity across all samples

Description

Divide each peptide/protein by the row mean/median and transform to log2

Usage

rowScaling(MSnSetObj, scalingFunction)

Arguments

MSnSetObj	MSnSet; an object of class MSnSet
scalingFunction	function; median or mean

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 <- rowScaling(MSnSet_data, scalingFunction=median)

crukci-bioinformatics/qPLEXanalyzer documentation built on Sept. 24, 2024, 1:13 a.m.