ENmix

ENmix performs preprocessing of Illumina Infinium HumanMethylation450 and MethylationEPIC BeadChip array data to correct dye-bias in DNA methylation estimation using the REgression on Logarithm of Internal Control probes (RELIC) method.

Key Features:

• Dye-Bias Correction: ENmix applies the RELIC method to correct performance differences between the two fluorescent dyes (Cy3-green/Cy5-red) used by Illumina Infinium HumanMethylation450 and MethylationEPIC BeadChips.
• Internal Control Probes: RELIC leverages intensity values from paired internal control probes that monitor the two color channels to enable array-wide bias correction.
• Performance Evaluation: RELIC has been evaluated against alternative dye-bias correction methods and reported to improve statistical significance and reliability of methylation measurements.
• Improved Data Quality: By reducing dye-related biases, ENmix improves the accuracy and reproducibility of CpG methylation estimates for downstream genomic analyses.

Scientific Applications:

• Epigenome-wide association studies (EWAS): Correction of dye-bias in Illumina Infinium HumanMethylation450 and MethylationEPIC BeadChip data to improve the reliability of DNA methylation estimates used in EWAS and related genomic research.

Methodology:

The RELIC method performs regression on the logarithm of paired internal control probe intensities to adjust for differential dye performance between Cy3 and Cy5 channels.