Estimate methylation M-value matrix

Estimate the methylation M-value matrix from a `MethyLumiM` or `eSet` object, which includes methylated and unmethylated probe intensities.

Usage

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

Arguments

methyLumiM

A [MethyLumiM-class] or `eSet` object, which includes methylated and unmethylated probe intensities.

returnType

Determines whether to return an `ExpressionSet` (`MethyLumiM` in this case) or a 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-values.

Details

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

Please check the lumi package for more details of the `estimateM` function.

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'.

Author

Pan Du