groupScaling: Normalization by scaling within group

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

Normalization by scaling within group

Description

Performs scaling normalization on the intensities within group (median or mean)

Usage

groupScaling(
  MSnSetObj,
  scalingFunction = median,
  groupingColumn = "SampleGroup"
)

Arguments

MSnSetObj	MSnSet; an object of class MSnSet
scalingFunction	function; median or mean
groupingColumn	character; the feature on which groups would be based; default="SampleGroup"

Details

In this normalization method the central tendencies (mean or median) of the samples within groups are aligned. The argument "groupingColumn" is used to define separate groups to normalize. The function takes one of the column of pData(data) as the variable for classifying group. The default variable is "SampleGroup". It is imperative in qPLEX-RIME experiment to define IgG as a separate group and normalize it separately from others. You could add a column into the metadata to define this classification.

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 <- groupScaling(MSnSet_data, 
                            scalingFunction=median, 
                            groupingColumn="SampleGroup")

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