I think I found a bug in the R package of "ChAMP". Even In its latest version, this bug were still existed there. As the following code shown in line 237 of function champ.lasso,
myDf <- data.frame(myDf, dmr.beta.means[,22:24]) #
Actually, I think it should be
myDf <- data.frame(myDf, dmr.beta.means[,17:19]) #
That's my opinion, I have contact the authors, However, there is no any response for long time. Is there any other friend found this problem/bug?
A: Package can be found here: http://www.bioconductor.org/packages/devel/bioc/html/ChAMP.html