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Messages - lawalo

1
CAMERA / Re: plotPsSpectrum error
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
CAMERA / plotPsSpectrum error
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
5
XCMS / Re: using plotPeaks to plot selected peaks
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
XCMS / using plotPeaks to plot selected peaks
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