easyEWAS Troubleshooting Guide

This guide provides a practical error index for easyEWAS.

1. Installation and dependency issues

Install easyEWAS from CRAN first. If you need the development version, you can install it from GitHub instead.

install.packages("easyEWAS")

install.packages(c("remotes", "BiocManager"))
BiocManager::install(c("sva", "clusterProfiler", "org.Hs.eg.db", "DMRcate"))

# Optional: install the latest development version from GitHub
remotes::install_github("ytwangZero/easyEWAS")

2. Data format and alignment issues

Rules:

• ExpoData first column: sample IDs
• MethyData first column: probe IDs
• MethyData sample columns must match ExpoData sample IDs

3. ComBat fails with prior plot

Try:

• plot = FALSE
• check NA patterns
• verify each batch has enough samples

4. DMR issues

Required genome/chip combinations:

• EPICV2 + hg38
• EPICV1 / 450K + hg19