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1
April 22, 2016, 03:37:50 PM
Hi Steffen, I used the script below on the WT files in the faahKO data. xset0 = xcmsSet(method="matchedFilter", fwhm=5, snthresh = 10, step = 0.01, steps = 1, max = 5) xset1 = group(xset0, bw = 3, minfrac = 0.9, mzwid = 0.05) xset2 = retcor(xset1, plottype = "mdevden") xset3 = group(xset2, bw = 3) xset4 = fillPeaks(xset3) xset4 = xsAnnotate(xset3) xset5 = groupFWHM(xset4, perfwhm = 0.6) xset6 = groupCorr(xset5, cor_eic_th=0.75, pval=0.05, calcCiS = TRUE, cor_exp_th=0.75) xset7 = findIsotopes(xset6) xset8 = findAdducts(xset7, polarity="positive") plotPsSpectrum(xset8, pspec=1, maxlabel=5) Error in if (!is.numeric(index) && index > length(sampnames(xs)) | index < : missing value where TRUE/FALSE needed Cheers, Mike
2
April 20, 2016, 05:00:58 AM
Hi Everyone, Just wondering if anyone has encountered an error while trying to plot a pseudospectra. plotEICs works just fine but plotPsSpectrum does not. The codes and error are posted below. Thanks in advance xset6 = xsAnnotate(xset5) xset7 = groupFWHM(xset6, perfwhm = 0.6) xset8 = groupCorr(xset7, cor_eic_th=0.75, pval=0.05, calcCiS = TRUE) xset9 = findIsotopes(xset8) xset10 = findAdducts(xset9, polarity="positive") plotEICs(xset10, pspec=6, maxlabel=5) plotPsSpectrum(xset10, pspec=6, maxlabel=5) Error in if (!is.numeric(index) && index > length(sampnames(xs)) | index < : missing value where TRUE/FALSE needed Cheers, Mike
3
June 10, 2015, 09:10:26 AM
played about and got it working! plotPeaks(xraw, mypeaks[seq(200,max(5, nrow(mypeaks))),], figs=c(2, 2)) Cheers again
4
June 10, 2015, 09:01:04 AM
if possible could you include an actual example. Cheers
5
June 10, 2015, 08:52:40 AM
Hi there, Thanks for getting back to me. I have some difficulty understanding the loop So this is what im working with below: library(xcms) list.files("/CDFs/20150414_Exp1d_3/new", recursive = TRUE) xraw = xcmsRaw("5TD_1.CDF", profstep = 1, profmethod = "bin", profparam = list(), includeMSn=FALSE, mslevel=NULL, scanrange=NULL) mypeaks = findPeaks.matchedFilter(xraw, fwhm=4, snthresh=10, step=0.1, steps=2) plotPeaks(xraw, mypeaks, figs=c(2, 2)) here is your suggestion: plotPeaks(xraw, p[seq(i,max(i+32, nrow(p))),], figs=c(10, 10)) i dont understand what seq, i, max, i+32, and nrow means if you could please elucidate on this. Thanks. BW, Sola
6
June 10, 2015, 06:51:14 AM
Hi all, I used plotPeaks to plot my xraw but it is only showing for the first few m/z. How do I set it to plot a peak that I am interested in. This is what I use: mypeaks = findPeaks.matchedFilter(xraw, snthresh=10, step=0.1, steps=2)) plotPeaks(xraw, mypeaks, figs=c(2, 2)) Thanks for your help in advance. Sola