varianceBeadStabilise: Bead level VST.

In blima: Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level

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.

Author(s)

Vojt<c4><9b>ch Kulvait

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 BiocManager::install('blimaTestingData').");
}

blima documentation built on Nov. 8, 2020, 8:15 p.m.