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]