blima (version 1.6.0)

bacgroundCorrect: Data background correction.

Description

Background correction procedure selecting beads with background Intensity I_b |mean - I_b | > k*SD(I_bs) for exclusion.

Usage

bacgroundCorrect(b, normalizationMod = NULL, channelBackground = "GrnB",  k = 3, channelBackgroundFilter = "bgf", channelAndVector = NULL)

Arguments

b

List of beadLevelData objects (or single object).

normalizationMod

NULL for normalization of 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.

channelBackground

Name of channel to normalize.

k

Parameter of method stringency (default is 3).

channelBackgroundFilter

Filtered beads will have weight 0 and non filtered weight 1.

channelAndVector

Represents vector to bitvise multiple to the channelBackgroundFilter vector.

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 biocLite('blimaTestingData').");
}