DAPAR (version 1.4.7)

diffAnaSave: Returns a MSnSet object with the results of the differential analysis performed with limma package.

Description

This method returns a 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

Examples

data(UPSpep25)
condition1 <- '25fmol'
condition2 <- '10fmol'
limma <- wrapper.diffAnaLimma(UPSpep25, condition1, condition2)
obj <- diffAnaSave(UPSpep25, limma, "limma", condition1, condition2)