backgroundChannelSubtract: Background channel subtraction

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

Description

Function to subtract one channel from another producing new channel. Standard graphic subtraction.

Usage

backgroundChannelSubtract(b, normalizationMod = NULL, channelSubtractFrom = "GrnF", 
    channelSubtractWhat = "GrnB", channelResult = "Grn")

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.
channelSubtractFrom	Name of channel to subtract from.
channelSubtractWhat	Name of channel to subtract.
channelResult	Result channel, if this channel exists it will be overwritten.

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.