wrapper.normalizeD: Normalisation

In prostarproteomics/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Normalisation

Description

Provides several methods to normalize quantitative data from a MSnSet object. They are organized in six main families : GlobalQuantileAlignement, sumByColumns, QuantileCentering, MeanCentering, LOESS, vsn For the first family, there is no type. For the five other families, two type categories are available : "Overall" which means that the value for each protein (ie line in the expression data tab) is computed over all the samples ; "within conditions" which means that the value for each protein (ie line in the Biobase::exprs() data tab) is computed condition by condition.

Usage

wrapper.normalizeD(obj, method, withTracking = FALSE, ...)

Arguments

obj	An object of class MSnSet.
method	One of the following : "GlobalQuantileAlignment" (for normalizations of important magnitude), "SumByColumns", "QuantileCentering", "Mean Centering", "LOESS" and "vsn".
withTracking	xxx
...	xxx

Value

xxx

Author(s)

Samuel Wieczorek, Thomas Burger, Helene Borges

Examples

data(Exp1_R25_pept, package="DAPARdata")
conds <- Biobase::pData(Exp1_R25_pept)$Condition
obj <- wrapper.normalizeD(
    obj = Exp1_R25_pept, method = "QuantileCentering",
    conds = conds, type = "within conditions"
)

prostarproteomics/DAPAR documentation built on Oct. 11, 2024, 12:03 p.m.