I think these are good general post-filtering options. However, your options depend on the type of hypothesis you are testing. Do you only want long blocks of differential methylation or do you believe that very localised methylation may also affect your phenotype? This will inform your cutoff for no.probes. Are you specifically looking at promoter methylation? If yes then taking only those with a gene symbol association makes sense.
Thanks for using DMRcate as intended and good luck!
I have used package called DMRcate to analyse 450k data. I want to find the gene which associates the DMRs.And I met some questions.The outputs include gene_assoc, group, hg19coord, no.probes, minpval, meanpval and maxbetafc,when I used the old version to analyse 450k data. But when I update the package,the outputs became coord, no.cpgs, minfdr, Stouffer, maxbetafc,meanbetafc.There is no result of "gene_assoc".I want to find the gene names associating "coord",can you help me ? Can you please tel me how to associate the gene by using the newest DMRcate packages.