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XCMS / rector() function error troubleshoot
I have encountered an issue when using xcms to analyze qTOF data. The R version I m using is 3.5.1 and the xcms version I have been using is 3.4.4.
Below are the steps I have taken to get this error with rector()...
- First I converted the Agilent qTOF data using MSConvert to mzXML file
- Next I extracted the mzXML file as following:
xset <- xcmsSet (mzmlfiles,
method = 'centWave',
ppm = 20,
mzdiff = -0.001,
peakwidth = c(5, 30))
xset <- group(xset)
xset_retcor <- retcor(xset)
The first two steps were passed, this error shows up with the third step:
xset_rector <- group(xset_retcor)
Performing retention time correction using 12250 peak groups.
Error in if (any(rtdevsmorange/rtdevrange > 2)) warn.overcorrect <- TRUE :
missing value where TRUE/FALSE needed
traceback() gives the following:
8: do_adjustRtime_peakGroups(peaks = peakmat, peakIndex = object@groupidx,
rtime = rtcor, minFraction = minFr, extraPeaks = extra, smooth = smooth,
span = span, family = family)
7: .local(object, ...)
6: retcor.peakgroups(object, ...)
5: retcor.peakgroups(object, ...)
4: do.call(method, alist(object, ...))
3: .local(object, ...)
2: retcor(xset)
1: retcor(xset)
Not sure if I am providing enough info to troubleshoot the problem, would really appreciate any suggetion why this error could happen!!