easyEWAS Troubleshooting Guide

This guide provides a practical error index for easyEWAS.

1. Installation and dependency issues

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