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Topic: Difference of minfrac and minsamp in group function (Read 5363 times) previous topic - next topic

Difference of minfrac and minsamp in group function

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

Re: Difference of minfrac and minsamp in group function

Reply #1
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...

 

Re: Difference of minfrac and minsamp in group function

Reply #2
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:

Code: [Select]
gcount >= classnum*minfrac & gcount >= minsamp

so both conditions are combined via logical AND.

Yours,
Steffen
--
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470
sneumann(at)IPB-Halle.DE