One thing that jumps at me is that you are aligning TOF data with a parameter setting for single quad (mzwid = 0.25 is default for group).
To my best understanding, there's a false setting for the parameters used in group function. How large is the proper mz width for TOF data? In XCMSOnline, 0.05 is the default for q-TOF data. I'll try this value first.
I'm a new user of XCMS and try to use it to process my LC-TOF data.
I have 28 samples which are devided into 'good' and 'bad' classes. The data were obtained by Agilent LC-TOF under a 90 minute long gradient condition. To me, only the data before about 58 minutes are meaningful. I cut therefor the peaklist off after the findPeak routine.
What makes me confused is that I found some zero intensity in the final results after diffreport. I checked my original data with Masshunter and those peaks actually exist in my EICs.
I have no idea about where the problem exist because there are a few steps before diffreport and a lot of corresponding parameters are involved. Follows are the codes I used for my data. Could somebody give me any suggestion?