Skip to main content


This section allows you to view all Topics made by this member. Note that you can only see Topics made in areas you currently have access to.

Topics - Jessica

XCMS / questions for peakgroup and sample class
Hi XCMSers,

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