wrapper.normalizeD {DAPAR} | R Documentation

## 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 `exprs()` data tab) is computed condition by condition.

### Usage

    wrapper.normalizeD(obj, method, type = NULL, scaling = FALSE,
      quantile = 0.15, span = 0.7)

### 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".
`type` | For the method "Global Alignment", the parameters are: "sum by columns": operates on the original scale (not the log2 one) and propose to normalize each abundance by the total abundance of the sample (so as to focus on the analyte proportions among each sample). "Alignment on all quantiles": proposes to align the quantiles of all the replicates; practically it amounts to replace abundances by order statistics. For the two other methods, the parameters are "overall" (shift all the sample distributions at once) or "within conditions" (shift the sample distributions within each condition at a time).
`scaling` | A boolean that indicates if the variance of the data have to be forced to unit (variance reduction) or not.
`quantile` | A float that corresponds to the quantile used to align the data.
`span` | parameter for LOESS method

### Value

An instance of class `MSnSet` where the quantitative data in the `exprs()` tab has been normalized.

### Author(s)

Samuel Wieczorek, Thomas Burger, Helene Borges

### Examples

    require(DAPARdata)
    data(Exp1_R25_pept)
    wrapper.normalizeD(Exp1_R25_pept[1:1000], "QuantileCentering", "within conditions")

[Package DAPAR version 1.16.11 Index]