beadarray (version 2.22.2)

limmaDE: Differential expression using limma

Description

Function to perform a standard limma analysis using a single command.

Usage

limmaDE(summaryData, SampleGroup, DesignMatrix = NULL, makeWts = TRUE, ...)

Arguments

summaryData

ExpressionSetIllumina object

SampleGroup

Name of column in phenoData that will be used to construct sample groups for analysis

DesignMatrix

Optional design matrix

makeWts

if TRUE weights will be calculated for each array

...

Other arguments that lmFit can accept

Value

a limmaResults object

Details

The function automates the steps used in a typical limma analysis. Firstly, the lmFit is used to fit a linear model from the specified column in phenoData. Array weights can be calculated (arrayWeights) and used in the fit. A contrast matrix of all possible contrasts is created (makeContrasts) and fitted (makeContrasts). The empirical Bayes shrinkage of variances is then applied (eBayes). The design matrix, contrast matrix and array weights can all be extracted for the resulting object.

Examples

if(require(beadarrayExampleData)){
  data(exampleSummaryData)
  rawdata <- channel(exampleSummaryData, "G")
  normdata <- normaliseIllumina(rawdata)
  limmaResults <- limmaDE(normdata, SampleGroup = "SampleFac")
  limmaResults
  DesignMatrix(limmaResults)
}