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XCMS / Re: diffreport gives retention time -1 for all groups
thanks for the fast reply.Still struggling with other stuff, but one problem less:-)
Thanks a lot!
Best regards,
Christine
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Messages - Christine
thanks for the fast reply.Still struggling with other stuff, but one problem less:-)
Thanks a lot!
Best regards,
Christine
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XCMS / diffreport gives retention time -1 for all groups
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)