doProbeTTests {blima} | R Documentation

## T-test for probe level data.

### Description

This function does aggregated probe level t-tests on the data provided by the object beadLevelData from package beadarray.

### Usage

    doProbeTTests(b, c1, c2, quality = "qua", channelInclude = "bgf",
        correction = "BY", transformation = NULL)

### Arguments

`b` | List of beadLevelData objects (or single object).
`c1` | List of logical vectors of data to assign to the first group (or single vector).
`c2` | List of logical vectors of data to assign to the second group (or single vector).
`quality` | Quality to analyze, default is "qua".
`channelInclude` | This field allows user to set channel with weights which have to be 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").
`correction` | Multiple testing adjustment method as defined by p.adjust function, default is "BY".
`transformation` | Function of input data trasformation, default is NULL. Any function which for input value returns transformed value may be supplied. T-test then will be evaluated on transformed data, consider use log2TranformPositive.

### Author(s)

Vojtěch Kulvait

### Examples

    if(require("blimaTestingData") && require("illuminaHumanv4.db") && interactive())
    {
        #To perform background correction, variance stabilization and  quantile normalization then test on probe level, bead level and print top 10 results.
        data(blimatesting)
        #Prepare logical vectors corresponding to conditions A(groups1Mod), E(groups2Mod) and both(processingMod).
        groups1 = "A";
        groups2 = "E";
        sampleNames = list()
        groups1Mod = list()
        groups2Mod = list()
        processingMod = list()
        for(i in 1:length(blimatesting))
        {
            p = pData(blimatesting[[i]]@experimentData$phenoData)
            groups1Mod[[i]] = p$Group %in% groups1;
            groups2Mod[[i]] = p$Group %in% groups2;
            processingMod[[i]] = p$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")
        beadTest = doTTests(blimatesting, groups1Mod, groups2Mod, "qua", "bgf")
        probeTest = doProbeTTests(blimatesting, groups1Mod, groups2Mod, "qua", "bgf")
        adrToSymbol <- merge(toTable(illuminaHumanv4ARRAYADDRESS), toTable(illuminaHumanv4SYMBOLREANNOTATED))
        adrToSymbol <- adrToSymbol[,c("ArrayAddress", "SymbolReannotated") ]
        colnames(adrToSymbol) <- c("Array_Address_Id", "Symbol")
        probeTestID = probeTest[,"ProbeID"]
        beadTestID = beadTest[,"ProbeID"]
        probeTestFC = abs(probeTest[,"mean1"]-probeTest[,"mean2"])
        beadTestFC = abs(beadTest[,"mean1"]-beadTest[,"mean2"])
        probeTestP = probeTest[,"adjustedp"]
        beadTestP = beadTest[,"adjustedp"]
        probeTestMeasure = (1-probeTestP)*probeTestFC
        beadTestMeasure = (1-beadTestP)*beadTestFC
        probeTest = cbind(probeTestID, probeTestMeasure)
        beadTest = cbind(beadTestID, beadTestMeasure)
        colnames(probeTest) <- c("ArrayAddressID", "difexPL")
        colnames(beadTest) <- c("ArrayAddressID", "difexBL")
        tocmp <- merge(probeTest, beadTest)
        tocmp = merge(tocmp, adrToSymbol, by.x="ArrayAddressID", by.y="Array_Address_Id")
        tocmp = tocmp[, c("ArrayAddressID", "Symbol", "difexPL", "difexBL")]
        sortPL = sort(-tocmp[,"difexPL"], index.return=TRUE)$ix
        sortBL = sort(-tocmp[,"difexBL"], index.return=TRUE)$ix
        beadTop10 = tocmp[sortBL[1:10],]
        probeTop10 = tocmp[sortPL[1:10],]
        print(beadTop10)
        print(probeTop10)
    }else
    {
        print("To run this example, please install blimaTestingData package from bioconductor by running BiocManager::install('blimaTestingData') and illuminaHumanv4.db by running BiocManager::install('illuminaHumanv4.db').");
    }

[Package blima version 1.22.0 Index]