Hi,

I read the the source code of champ.DMR, I find the words:

    X <- cbind(1,(as.numeric(as.factor(pheno))-1))
    print(nrow(x))
    Beta <- beta[bumphunter.idx,]
    Beta <- replace(Beta,which(Beta <= 0.001),0.001)
    Beta <- replace(Beta,which(Beta >= 0.999),0.999)
    Y <- log((Beta/(1-Beta)),2)

    Bumps <- bumphunter(Y,
                        design=X,
                        chr=Anno[bumphunter.idx,]$chr,
                        ......

Does the DMR not still support the multi-phenotypes with the "bumphunter" method ? And I could not also find the compare.groups setting here. Do anyone know that? Thank!

the version of ChAMP is 2.16.1

Best,

Lei

Hi Lei:

Sorry that ChAMP does not support multil-phenotype yet. But indeed it's a feature should be improved.

Best Tian