I have 2 questions for xcms.
1. Is there relation between minfrac and minsamp in xcms::group.density step? For example, if I have two classes and each class contains 6 samples. If my minfrac is set at 0.5, must I set my minsamp to 3?
2. My data is a little complex. I have 2 classes, control and treatment. Each class has 9 subclasses of time and each subclasses has 5 samples. At first, I created just 2 folders for 2 classes (45 samples for 1 file), and I applied xcms. 1090 peak groups were found. Then, I tried to subdivide samples. I created 9 subfolders in every folders and each subfolder contians just 5 samples. I reapplied xcms with the same script, but this time only 251peaks groups were found. So I don't know for my experiment, which way is better for me?
Do you have some ideas?
Thank you very much in advance