selectedChannelTransform: Channel transformation

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

Description

Function to transform channel data.

Usage

selectedChannelTransform(b, normalizationMod = NULL, channelTransformFrom, 
    channelResult, transformation = NULL)

Arguments

b	List of beadLevelData objects (or single object).
normalizationMod	NULL for performing on all input b. Otherwise specifies logical vector of the length equals to the number of arrays in b or list of such vectors if b is a list of beadLevelData classes.
channelTransformFrom	Name of channel to transform.
channelResult	Result channel, if this channel exists it will be overwritten.
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)

Vojt<c4><9b>ch Kulvait

Examples

if(require("blimaTestingData") && interactive())
{
    #To perform background correction on blimatesting object for two groups. Background correction is followed by correction for non positive data. Array spots out of selected groups will not be processed.
    data(blimatesting)
    #Prepare logical vectors corresponding to conditions A and E.
    groups1 = "A";
    groups2 = "E";
    sampleNames = list()
    c = list()
    for(i in 1:length(blimatesting))
    {
        p = pData(blimatesting[[i]]@experimentData$phenoData)
        c[[i]] = p$Group %in% c(groups1, groups2);
        sampleNames[[i]] = p$Name
    }
    #Background correction and quantile normalization followed by testing including log2TransformPositive transformation.
    blimatesting = bacgroundCorrect(blimatesting, normalizationMod=c, channelBackgroundFilter="bgf")
    blimatesting = nonPositiveCorrect(blimatesting, normalizationMod=c, channelCorrect="GrnF",  channelBackgroundFilter="bgf", channelAndVector="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.