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Topic: What's definition of density in the process of group? (Read 4671 times) previous topic - next topic

What's definition of density in the process of group?

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

Re: What's definition of density in the process of group?

Reply #1 –
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
Quote
peaks are plotted as points showing relative intensity. identified groups are flanked by dotted vertical lines.