XCMS fillPeaks.MSW

July 29, 2016, 08:41:59 AM

I am extracting my peaks from direct infusion Orbitrap mass spectrometry data using R and the xcms package. Currently I have 52 spectra divided into 8 seperate classes. I am trying to use the fill peaks function using the mass spectra wavelet method to extract missing data. This results in the the error message below

Error in seq.default((mmzpos - mrange[1]), (mmzpos + mrange[2])) :
'from' must be of length 1

I am not sure what is causing this error message to occur or how to fix it.

Xset<-xcmsSet(method="MSW", files=msFiles, scales=c(1,4,9),nearbyPeak=T, verbose.columns = FALSE, winSize.noise=500,
SNR.method="data.mean",snthr=5)
XsetG<-group(Xset, method="mzClust", mzppm=5)
XsetGf<-fillPeaks(XsetG, method="MSW")

Also using the xcmsSet function I am finding I get warning messages for each spectra

39: In `[<-`(`*tmp*`, "object", value = <S4 object of class structure("xcmsRaw", package = "xcms")>) :
implicit list embedding of S4 objects is deprecated