XCMS pair-wise processing error when switching which is control data set

I have used XCMS for many months for pairwise analysis of 5 combined control vs 5 combined experimental. I noticed a problem with pairwise MS analysis because no matter which data set I used as the control, I got identical results for control A vs B or control B vs A. I expected that these 2 tests would provide opposite results. I contacted XCMS several times and never received an explanation. I'm asking that you submit 2 MS data sets with identical conditions of 2 different samples for pairwise analysis and switch the controls to see if you also get identical or opposite results. With so many researchers submitting data for comparing experimental vs control this would be a serious problem.


Do you use XCMS through Galaxy / W4M ?