Dear xcms developers,
I would be grateful if you could explain the difference between the minfrac and minsamp parameters in the group function of xcms. A small example would also be appreciated. I believe I correctly understand the minfrac parameter (the "percentage" of samples that need to have proper peaks under a group so as to define a meta-peak?), but can you please also explain the minsamp parameter? In addition, if the minsamp parameter is increased, naturally the number of peak groups decreases. How advisable/useful is to increase minsamp in a dataset of 75 samples but including 16 different classes? (CE/MS). Thank you in advance for your help.
Panos
Do these parameters exclude each other? That is the user can use either minfrac either minsamp, depending on whether he/she wants to constrain based on percentage or absolute number of samples in each group? Probably...
Hi,
both minsamp and minfrac lead to a number of minimum samples where a peak
has to be present to become a group. minsamp has an advantage if you have
sampleclasses with different numbers of samples, and you want to "fix" the
number of samples required. The relevant code reads:
gcount >= classnum*minfrac & gcount >= minsamp
so both conditions are combined via logical AND.
Yours,
Steffen