DAPAR (version 1.4.7)

diffAna: 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)

Examples

data(UPSpep25)
qData <- Biobase::exprs(UPSpep25)
design <- cbind(cond1=1, cond2 = rep(0,nrow(Biobase::pData(UPSpep25))))
rownames(design) <- rownames(Biobase::pData(UPSpep25))
labels <- Biobase::pData(UPSpep25)[,"Label"]
indices <- getIndicesConditions(labels, "25fmol", "10fmol")
design[indices$iCond2,2] <- 1
diffAna(qData, design)