diffreport gives retention time -1 for all groups

January 09, 2013, 05:43:57 AM

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)

Re: diffreport gives retention time -1 for all groups

Reply #1 – January 09, 2013, 07:14:20 AM

Hi,

mzClust is specifically designed for direct infusion single spectra
and completely ignores the retention time.

Quote

groupedxset1 = group(xset1, method="mzClust", mzppm=3)

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

Re: diffreport gives retention time -1 for all groups

Reply #2 – January 22, 2013, 09:59:07 AM

Hi Stefan,
thanks for the fast reply.Still struggling with other stuff, but one problem less:-)
Thanks a lot!
Best regards,
Christine