Dear Fei, comparisons of groups with different numbers of samples should not be a problem. You are referring to a different number of genomic regions tested for. Please create MEDIPS SETs or MEDIPSroiSets with the same parameter settings so that the resulting coverage vectors have the same length. Combining a MEDIPS SET for e.g. 500bp windows genome wide with a MEDIPSroiSet created for e.g. promoter regions only, is not possible. I hope this helps. All the best, Lukas On 12 Jan 2017, at 10:41, fmhsu0114 [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 fmhsu0114<https: support.bioconductor.org="" u="" 12157=""/> wrote Question: MEDIPS: case study with different replicate numbers of control and case<https: support.bioconductor.org="" p="" 91110=""/>: Dear all, I'm using MEDIPS to process MBD-seq data, with 2 control replicates and 3 case replicates. It seems that the MEDIPS.meth function needs same length of MSet (I got error message 'MEDIPSset/MEDIPSroiSet objects are of different length'). Any advice for this issue? I can use the MEDIPS.mergeSets, but this will make the replicates into one. Thanks in advance, Fei ________________________________ Post tags: MEDIPS You may reply via email or visit MEDIPS: case study with different replicate numbers of control and case