diffAna {DAPAR} | R Documentation

## This function performs a differential analysis on an MSnSet object (adapted from `limma`)

### Description

Performs a differential analysis on an `MSnSet` object, based on `limma` functions.

### Usage

    diffAna(qData, design)

### Arguments

`qData` | A dataframe that contains quantitative data.
`design` | The design matrix as described in the limma package documentation

### Value

A dataframe with the p-value and log(Fold Change) associated to each element (peptide/protein)

### Author(s)

Florence Combes, Samuel Wieczorek

### Examples

    require(DAPARdata)
    data(Exp1_R25_pept)
    qData <- Biobase::exprs(Exp1_R25_pept[1:1000])
    design <- cbind(cond1=1,
    cond2 = rep(0,nrow(Biobase::pData(Exp1_R25_pept[1:1000]))))
    rownames(design) <- rownames(Biobase::pData(Exp1_R25_pept[1:1000]))
    labels <- Biobase::pData(Exp1_R25_pept[1:1000])[,"Label"]
    indices <- getIndicesConditions(labels, "25fmol", "10fmol")
    design[indices$iCond2,2] <- 1
    diffAna(qData, design)

[Package DAPAR version 1.10.4 Index]