blima (version 1.6.0)

varianceBeadStabilise: Bead level VST.

Description

This function does variance stabilising step on bead level.

Usage

varianceBeadStabilise(b, normalizationMod = NULL, quality = "qua",  channelInclude = "bgf", channelOutput = "vst")

Arguments

b

List of beadLevelData objects (or single object).

normalizationMod

NULL for normalization of all input b. Otherwise specifies logical vector of the length equal to the number of arrays in b or list of such vectors if b is a list of beadLevelData classes.

quality

Quality to analyze, default is "qua".

channelInclude

This field allows user to set channel with weights which have to be in 0,1. All zero weighted items are excluded from t-test. You can turn this off by setting this NULL. This option may be used together with bacgroundCorrect method or/and with beadarray QC (defaults to "bgf").

channelOutput

Output from VST.

Examples

if(require("blimaTestingData") && interactive())
{
    #To perform background correction, variance stabilization and quantile normalization.
    data(blimatesting)
    #Prepare logical vectors corresponding to conditions A(groups1Mod), E(groups2Mod) and both(c).
    groups1 = "A";
    groups2 = "E";
    sampleNames = list()
    processingMod = list()
    for(i in 1:length(blimatesting))
    {
        p = pData(blimatesting[[i]]@experimentData$phenoData)
        processingMod[[i]] = p$Group %in% c(groups1, groups2);
        sampleNames[[i]] = p$Name
    }
    #Background correction and quantile normalization followed by testing including log2TransformPositive transformation.
    blimatesting = bacgroundCorrect(blimatesting, normalizationMod = processingMod, channelBackgroundFilter="bgf")
    blimatesting = nonPositiveCorrect(blimatesting, normalizationMod = processingMod, channelCorrect="GrnF",  channelBackgroundFilter="bgf", channelAndVector="bgf")
    blimatesting = varianceBeadStabilise(blimatesting, normalizationMod = processingMod,
            quality="GrnF", channelInclude="bgf", channelOutput="vst")
    blimatesting = quantileNormalize(blimatesting, normalizationMod = processingMod,
            channelNormalize="vst", channelOutput="qua", channelInclude="bgf")
}else
{
    print("To run this example, please install blimaTestingData package from bioconductor by running biocLite('blimaTestingData').");
}