batch correction using control probe

[bioinfonext]

Hi all,

I am trying to use below script for batch correction for epic array data, but not sure what R packages need for controlVariation() function? or is there another way to correct for batch effect using control probes

Load the required libraries:

library(RnBeads)
library(minfi)
library(IlluminaHumanMethylationEPICanno.ilm10b2.hg19)

Import the methylation data and sample information:

samples <- read.table("sample_table.txt", header=TRUE)
methylation_data <- read.metharray.exp("methylation_data.txt")
methylation_data <- as.matrix(methylation_data[, -1]) # Remove the first column (IDs)
colnames(methylation_data) <- samples$ID # Rename the columns with sample IDs

Preprocess the methylation data:

methylation_data <- preprocessMethylationSet(methylation_data)

Extract the control probes:

control_probes <- getEpicControlProbeIDs()
methylation_data_control <- methylation_data[control_probes, ]

Normalize the control data:
methylation_data_control <- preprocessRaw(methylation_data_control, bg.correct=TRUE, normalize="controls")

Estimate the technical variation:

control_stats <- controlVariation(methylation_data_control)

Correct for batch effects in the methylation data:

methylation_data_corrected <- preprocessRaw(methylation_data, bg.correct=TRUE, normalize="controls", control.stats=control_stats)

Many thanks, bioinfo