| varianceBeadStabilise {blima} | R Documentation |
This function does variance stabilising step on bead level.
varianceBeadStabilise(b, normalizationMod = NULL, quality = "qua",
channelInclude = "bgf", channelOutput = "vst")
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. |
Vojtěch Kulvait
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').");
}