Hi to all,
I have some problems comparing group.density and group.mzClust methods or maybe I didn't well understand th way group.mzClust works.
Indeed, when I group according to density method the diffreport is well composed of mz and rt data while with mzClust rtmed, rtmin and rtmax have only -1 value for all extracted ions.
is it normal ?
I point out that I work on HPLC-QTOF data.
here below you can find the scripts I used:
group.density
xset <- xcmsSet(method="matchedFilter", fwhm=10, snthresh=3, nSlaves=4)
xsetb <- group(xset, minfrac = 0.75, bw = 10)
xset2 <- retcor(xsetb, family="s", plottype="m")
xset2b <- group(xset2, minfrac = 0.50, bw = 5)
xset3 <- fillPeaks(xset2b)
reporttabACP <- diffreport(xset3, "A", "B", "groupdensity7550", 1000)
group.mzClust
xset <- xcmsSet(method="matchedFilter", fwhm=10, snthresh=3, nSlaves=4)
xsetb <- group(xset, method="mzClust", mzppm=25)
xset2 <- retcor(xsetb, family="s", plottype="m")
xset2b <- group(xset2, method="mzClust", mzppm=25)
xset3 <- fillPeaks(xset2b)
reporttabACP <- diffreport(xset3, "A", "B", "groupmzClust", 1000)
thanks for your help.