ChAMP is a very useful package on Illumina 450k human methylation chips, and I have used it for several times. However, ChAMP requires that the "sample group" is written in the SampleSheet.csv, and uses it to divide the samples into "test" and "control", therefore its hypothesis test is made between this two groups. But this time I want to do paired test, for my samples consist of certain people each before and after taking drug. So the test and control must be paired by people. And I still want to use the tools in ChAMP package such as MVP tools and Probe Lasso tools, for they are very useful and can give well-presented results. Is there any option in ChAMP for doing paired test?

Thank you very much!