Question: How can I define which samples are controls and which samples are cases in ChAMP
gravatar for yuabrahamliu
12 months ago by
yuabrahamliu0 wrote:

Hi there,

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.

Best wishes,



ADD COMMENTlink modified 12 months ago • written 12 months ago by yuabrahamliu0

Hello Yu:

champ.DMP() can only assign "comparegroup", which means you tell program which two phenotypes you want to compare, then the program would automatically ORDER them by their name. So sorry that champ.DMP() can not assign case/control.

However, in the analysis view, the result of DMP should be exactly the same despite of the directions. The DMPs you find via comparing case to control, should also be DMPs you find by comparing control to case. 

You just need to manually add negative sign on the logFC/t statistic, then it should be correct.

By the way, you may also send email to for ChAMP questions in the future.


Yuan Tian

ADD REPLYlink written 12 months ago by Yuan Tian120

I see. Thank you Yuan!

ADD REPLYlink written 12 months ago by yuabrahamliu0
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