estimateM: Estimate methylation M-value matrix

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

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)

lumi documentation built on Nov. 8, 2020, 5:27 p.m.