lumi (version 2.24.0)

estimateM: 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

Value

A MethyLumiM or matrix object of methylation 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.

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)