rector() function error troubleshoot October 15, 2020, 06:16:29 PM Hello everyone,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 neededtraceback() 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!! Quote Selected
Re: rector() function error troubleshoot Reply #1 – October 16, 2020, 04:02:41 PM Here is an update to this topic - it seems that the steps in this question is a bit outdated...I eventually tried to use the most updated xcms package (3.10.2) and peak grouping worked fine with readMSData() and chromatogram()!! Quote Selected