This study compares the Beta-value and M-value methods for quantifying methylation levels using microarray analysis. The Beta-value, recommended by Illumina, ranges from 0 to 1 and is interpreted as the percentage of methylation. The M-value, calculated as the log2 ratio of methylated to unmethylated probe intensities, is more statistically valid but lacks an intuitive biological interpretation. The relationship between Beta-value and M-value is shown to be a Logit transformation, with Beta-value having severe heteroscedasticity for highly methylated or unmethylated CpG sites. A methylation titration experiment was designed to evaluate the performance of both methods in identifying differentially methylated CpG sites. Results indicate that the M-value method performs better in terms of Detection Rate (DR) and True Positive Rate (TPR) for both highly methylated and unmethylated CpG sites. Imposing a minimum threshold of difference improves the performance of the M-value method but not the Beta-value method. The study recommends using the M-value method for differential methylation analysis and including the Beta-value statistics in final reports due to its intuitive biological interpretation.This study compares the Beta-value and M-value methods for quantifying methylation levels using microarray analysis. The Beta-value, recommended by Illumina, ranges from 0 to 1 and is interpreted as the percentage of methylation. The M-value, calculated as the log2 ratio of methylated to unmethylated probe intensities, is more statistically valid but lacks an intuitive biological interpretation. The relationship between Beta-value and M-value is shown to be a Logit transformation, with Beta-value having severe heteroscedasticity for highly methylated or unmethylated CpG sites. A methylation titration experiment was designed to evaluate the performance of both methods in identifying differentially methylated CpG sites. Results indicate that the M-value method performs better in terms of Detection Rate (DR) and True Positive Rate (TPR) for both highly methylated and unmethylated CpG sites. Imposing a minimum threshold of difference improves the performance of the M-value method but not the Beta-value method. The study recommends using the M-value method for differential methylation analysis and including the Beta-value statistics in final reports due to its intuitive biological interpretation.