adjColorBias.ssn {lumi} | R Documentation

## Color bias adjustment of Illumina Infinium methylaton microarrays using simple shift and scaling normalization

### Description

Color bias adjustment of Illumina Infinium methylaton microarrays using simple shift and scaling normalization

### Usage

    adjColorBias.ssn(methyLumiM, refChannel = c("green", "red", "mean"))

### Arguments

`methyLumiM` | a MethyLumiM object or any eSet object with "methylated" and "unmethylated" data matrix element in the assayData slot
`refChannel` | the reference color channel for color bias adjustment

### Details

Perform color bias adjustment of Illumina Infinium methylaton microarrays. It requires the input methyLumiM object includes the color channel information in the featureData. Basically, there should be a "COLOR_CHANNEL" column in the data.frame returned by pData(featureData(methyLumiM)).

The basic idea of color bias adjustment is to treat it as the normalization between two color channels. It uses simple scaling normalization to normalize two color channels. The background levels are estimated using function `estimateMethylationBG`.

### Value

Return an object (same class as input methyLumiM) with updated "methylated" and "unmethylated" data matrix after color bias adjustment.

### Author(s)

Pan DU

### See Also

See Also `lumiMethyC`, `estimateMethylationBG` and `adjColorBias.quantile`

### Examples

    data(example.lumiMethy)
    # before adjustment
    plotColorBias1D(example.lumiMethy)
    lumiMethy.adj = adjColorBias.ssn(example.lumiMethy)
    # after adjustment
    plotColorBias1D(lumiMethy.adj)

[Package lumi version 2.40.0 Index]