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XCMS / Identified features does not match mz values in raw files
What could be the explanation for this?
I am using RStudio (Version 0.98.994), XCMS (version 1.38.0).
I have a HPLC-qTOF (Bruker) which produces .d files. I have converted these files into .mzXML files by CompassXport 3.0.
Following I run
Code: [Select]
library(xcms)
xset <- xcmsSet(myDir, ppm = 30, peakwidth = c(10,60), method = "centWave", snthresh = 10, noise=100, prefilter = c(4,1000),
mzCenterFun = "wMean", integrate = 1, mzdiff=-0.01, fitgauss = TRUE, profparam = list("step" = 0.01))
xset1 <- group(xset, bw = 30, minfrac = 0.5, minsamp = 1, mzwid = 0.025, max = 50)
xset2 <- retcor(xset1, missing = 1, extra = 1, smooth = "loess", span = 0.2, family = "symmetric")
xset3 <- group(xset2, bw = 30, minfrac = 0.5, minsamp = 1, mzwid = 0.025, max = 50)
xset4 <- fillPeaks.chrom(xset3)
reporttab <- diffreport(xset4, "A", "B", "Outputfile2", 11, metlin = 0.15, h = 480, w = 640)
xset5 <- peakTable(xset4, filebase="name")
Any help is really appreciated!