Deal all,
As mentioned of XCMS preprocessing document, the argument of group(), sleep, is enabled to plot the corresponding peaks. My questions are:
1. Is the method "density" the default grouping ?
2. What's the definition of density (Y-axis)? Is it normalized? If YES, what is the value normalized? Why the corresponding value is usually small?
3. What's the definition of the solid line in this figure? Peaks are plotted as points showing it relative intensity. And what's meaning of the solid line?
Thank you for your reply. :)
Best regards,
Hsiang
Yes, density is the default method for group.
The density is the result of an kernel density estimation (?density), see Colin's original XCMS paper.
also see ?group.density