estimateM {lumi} | R Documentation

## Estimate methylation M-value matrix

### Description

Estimate methylation M-value matrix from MethyLumiM-class object or eSet-class object, which include methylated and unmethylated probe intensities

### Usage

    estimateM(methyLumiM, returnType=c("ExpressionSet", "matrix"), offset=100)

### Arguments

`methyLumiM` | MethyLumiM-class object or eSet-class object, which include methylated and unmethylated probe intensities
`returnType` | determine whether return an ExpressionSet (MethyLumiM in this case) or matrix object
`offset` | offset added to the methylated and unmethylated probe intensities when estimating the M-value

### Details

M-value is the log2 ratio between Illumina methylated and unmethylated probe intensities. As variations of small intensities can cause big changes in the ratio estimation, so an offset is added to methylated and unmethylated probe intensities when estimating the M-value.

### Value

A MethyLumiM or matrix object of methylation M-value

### Author(s)

Pan DU

### References

Du, P., Zhang, X, Huang, C.C., Jafari, N., Kibbe, W.A., Hou, L., and Lin, S.M., (2010) 'Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis', (under review)

### See Also

See Also as `estimateBeta`, `estimateIntensity`

### Examples

    data(example.lumiMethy)
    methyLumiM = estimateM(example.lumiMethy)
    boxplot(methyLumiM)

[Package lumi version 2.36.0 Index]