1
XCMS / Integration
I am a relatively new user of XCMS .I have a few questions regarding XCMS integration and hope you can help me with your expertise.
1.
The description of diffreport-method says that the default argument for value is "into", so the integrated peak intensities (raw) are used. Is it really the integrated peak intensity or the integrated peak area which is used to find statistically significant differences between two samples?
2.
Is it possible to use the integrated area of filtered peak instead of using the integrated area of raw peak in diffreport to find the most statistically significant differences between two samples and what parameter must be changed in the code (I pasted my code below)?
I use R version 2.15.3 (2013-03-01), xcms_1.34.0 mzR_1.4.7, Rcpp_0.10.4
Used code:
library(xcms)
library(mzR)
library(Rcpp)
xset=xcmsSet(snthresh=8, profmethod="binlin")
xset
xset=group(xset, bw=20)
xset2=retcor(xset,family="symmetric",plottype="mdevden")
xset2=group(xset2,bw=10)
xset3=fillPeaks(xset2)
xset3
reporttab=diffreport(xset3,"NE","PO","example",9000)
reporttab [1:9000]
Thank you very much!
Best regards!!
Johannes