Dear mtefit, MEDIPS does not allow to analyze multiple (>2) conditions. Please consider our R/BioC package qsea, which also has MeDIP-seq specific functionalities but also allows the use of a design matrix. Sincerely, Lukas _____________________________________ Lukas Chavez, Ph.D. Assistant Professor, Department of Medicine University of California, San Diego (UCSD) Biomedical Research Facility 2 | Room 2A24 9500 Gilman Drive | MC 0765 | La Jolla, CA 92093 T: 858 246 1919 | Email: lukaschavez@ucsd.edu<mailto:lukaschavez@ucsd.edu> www.oncoepigenomics.org<http: www.oncoepigenomics.org=""> On Nov 28, 2018, at 3:47 PM, mtefit [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User mtefit<https: support.bioconductor.org="" u="" 18571=""/> wrote Question: Comparing more than 2 experimental groups with MEDIPS?<https: support.bioconductor.org="" p="" 115611=""/>: I am using MEDIPS to analyze MEDIP-seq data but I need to compare multiple conditions. Is it possible to use this package to detect differential coverage between more than 2 experimental conditions? ________________________________ Post tags: medips, medip-seq, dna methylation, dmr analysis You may reply via email or visit Comparing more than 2 experimental groups with MEDIPS?