Hi,
I am processing my data with XCMS and it seems to work out so far untill I try to export the data by the function diffreport. In the exported table the retention time for each peak is -1. A more experienced R user checked already all sets. The retention time ist still valid and existing in xSet3.
Does someone has an idea, why the loss/-1 retention time occures?
Thanks a lot in advance!
Christine
My script:
xset = xcmsSet(files = path, snames = NULL, sclass = NULL, phenoData = NULL, method="centWave", ppm=5,
peakwidth=c(3,4.5),
snthresh=15,
prefilter=c(3,2000),
mzCenterFun="meanApex3",
integrate=1,
mzdiff=0.005,
fitgauss=FALSE)
groupedxset = group(xset, method="mzClust", mzppm=3)
xset1 = retcor(groupedxset, family = "s",span=0.2)
groupedxset1 = group(xset1, method="mzClust", mzppm=3)
xset3 = fillPeaks(groupedxset1)
reporttab = diffreport(xset3,class1 = levels(sampclass(xset3))[1], class2 = levels(sampclass(xset3))[2],"XCMS 130108_5",20,metlin=0.15)
Hi,
mzClust is specifically designed for direct infusion single spectra
and completely ignores the retention time.
I'd have to think whether and how to actually report the RT,
if peaks in one group appear from all over the chromatography
because they have the same m/z.
Yours,
Steffen
Hi Stefan,
thanks for the fast reply.Still struggling with other stuff, but one problem less:-)
Thanks a lot!
Best regards,
Christine