I have a question about ChAMP again. After I used champ.DMP to find the differential methylated probes successfully. I deemed the probes with a minus logFC as hypo ones (their methylation level was lower in cases than controls), while that with a plus logFC as hyper ones (their methylation level was higher in cases than controls). However, when I checked them manually, I found actually, the DMPs with a minus logFC had a lower level in controls, not in cases, which was totally contrary to what was expected by me, so was it mean that I reversed the sample labels when using champ.DMP? Actually I didn't find a parameter here used to assign which samples belong to the case group and which ones belong to the control group. This information was only contained in the SampleSheet.csv file when I loaded the data at the beginning. Hence, I am wondering is it necessary to define the sample group by myself in the champ.DMP step, so that I could guarantee that the control group samples were used as references, not the case group as references? and how can I do that? Thank you so much.