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XCMS Online / Questions about LCMS data preprocessing R vignette
I have two questions on the vignette for the xcms R package, 'LCMS data preprocessing and analysis with xcms.'
In the vignette it says "We set it to 20,80 for the present example data set" when referring to the peakwidth parameter for centWave, but in the actual function they use 30,80. This makes a big difference in the Faahko data set, which is recommended?
Why do they use minFraction = 0.8 for PeakDensityParam but minFraction = 0.85 for PeakGroupsParam?