Hi Everyone,

I am currently working on a differential methylation analysis using the champ.DMP function from the ChAMP package in R. Despite receiving a message indicating a large number of significant MVPs (157,948 with BH adjusted p-values below 0.05), the resulting myDMP object is empty. why?

Context: Dataset: I am analyzing a beta matrix from Illumina Human Methylation EPIC Beadchip data. Phenotype Data: The dataset includes samples categorized into two groups: MILD and SEVERE.

sample_names <- colnames(beta_matrix)
sample_groups <- ifelse(grepl("SEVERE", sample_names), "SEVERE", "MILD")
sample_info <- data.frame(Sample = sample_names, Group = sample_groups, stringsAsFactors = FALSE)
phenotype <- factor(sample_info$Group, levels = c("MILD", "SEVERE"))

myDMP <- champ.DMP(beta = beta_matrix, pheno = phenotype, arraytype = "EPIC")