relic: RELIC dye bias correction method for Illumina...

In USCbiostats/ENmixUSC: Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)

Description

REgression on Logarithm of Internal Control probes (RELIC) correct for dye bias on whole array by utilizing the intensity values of paired internal control probes that monitor the two color channels.

Usage

relic (mdat,at_red,cg_grn)

Arguments

mdat	An object of class MethylSet.
at_red	an intensity matrix for Illumina control probes "NORM_A" and "NORM_T"
cg_grn	an intensity matrix for Illumina control probes "NORM_C" and "NORM_G"

Details

The Illumina MethylationEPIC BeadChip contains 85 pairs of internal normalization control probes (name with prefix NORM_A, NORM_T, NORM_G or NORM_C), while its predecessor, Illumina HumanMethyl-ation450 BeadChip contains 93 pairs. RELIC first performs a regression on the logarithms of the intensity values of the normalization control probes to derive a quantitative relationship between red and green channels, and then uses the relation-ship to correct for dye-bias on intensity values for whole array.

Value

An object of class MethylSet

Author(s)

Zongli Xu and Liang Niu

References

Zongli Xu, Sabine A. S. Langie, Patrick De Boever, Jack A. Taylor and Liang Niu, RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip, in review 2016

See Also

Package preprocessENmix

Examples

if(FALSE){
if (require(minfiData)) {
    #background correction and dye bias correction
    mdat <- preprocessENmix(RGsetEx,bgParaEst="oob",nCores=6,dyeCorr =="RELIC")
    #dye bias correction only
    ctrls <- getProbeInfo(RGsetEx,type="Control")
    ctrls <- ctrls[ctrls$Address %in% featureNames(RGsetEx),]
    ctrl_r <- getRed(RGsetEx)[ctrls$Address,]
    ctrl_g <- getGreen(RGsetEx)[ctrls$Address,]
    CG.controls <- ctrls$Type %in% c("NORM_C","NORM_G")
    AT.controls <- ctrls$Type %in% c("NORM_A","NORM_T")
    cg_grn <- ctrl_g[CG.controls,]
    rownames(cg_grn) = ctrls$ExtendedType[CG.controls]
    at_red <- ctrl_r[AT.controls,]
    rownames(at_red) = ctrls$ExtendedType[AT.controls]
    mdat <- preprocessRaw(RGsetEx)
    mdat <- relic(mdat,at_red,cg_grn)
}}

USCbiostats/ENmixUSC documentation built on June 1, 2019, 3:55 a.m.