nonPositiveCorrect {blima} | R Documentation

## Correct non positive

### Description

Correction for positive values only

### Usage

    nonPositiveCorrect(b, normalizationMod = NULL, channelCorrect = "GrnF",
        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.
`channelCorrect` | Name of channel to correct.
`channelBackgroundFilter` | Filtered beads will have weight 0 and non filtered weight 1.
`channelAndVector` | Represents vector to bitvise multiple to the channelBackgroundFilter vector.

### Author(s)

Vojtěch 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').");
    }

[Package blima version 1.22.0 Index]