diffAnaSave {DAPAR} | R Documentation

## Returns a `MSnSet` object with the results of the differential analysis performed with `limma` package.

### Description

This method returns a class `MSnSet` object with the results of differential analysis.

### Usage

    diffAnaSave(obj, data, method = "limma", condition1, condition2,
      threshold_pVal = 1e-60, threshold_logFC = 0, fdr = 0,
      calibrationMethod = "pounds")

### Arguments

`obj` | An object of class `MSnSet`.
`data` | The result of the differential analysis processed by `diffAna`
`method` | The method used for differential analysis. Available choices are : "limma", "Welch"
`condition1` | A vector containing the names (some values of the slot "Label" of `pData()` of the first condition.
`condition2` | A vector containing the names (some values of the slot "Label" of `pData()` of the second condition.
`threshold_pVal` | A float that indicates the threshold on p-value choosen to discriminate differential proteins.
`threshold_logFC` | A float that indicates the threshold on log(Fold Change) to discriminatedifferential proteins.
`fdr` | The FDR based on the values of threshold_pVal and threshold_logFC
`calibrationMethod` | The calibration method used to compute the calibration plot

### Value

A MSnSet

### Author(s)

Alexia Dorffer, Samuel Wieczorek

### Examples

    require(DAPARdata)
    data(Exp1_R25_pept)
    condition1 <- '25fmol'
    condition2 <- '10fmol'
    limma <- wrapper.diffAnaLimma(Exp1_R25_pept[1:1000],
    condition1, condition2)
    obj <- diffAnaSave(Exp1_R25_pept[1:1000], limma, "limma",
    condition1, condition2)

[Package DAPAR version 1.10.4 Index]