Hi all,
I'm a new user of XCMS and try to use it to process my LC-TOF data.
I have 28 samples which are devided into 'good' and 'bad' classes. The data were obtained by Agilent LC-TOF under a 90 minute long gradient condition. To me, only the data before about 58 minutes are meaningful. I cut therefor the peaklist off after the findPeak routine.
What makes me confused is that I found some zero intensity in the final results after diffreport. I checked my original data with Masshunter and those peaks actually exist in my EICs.
I have no idea about where the problem exist because there are a few steps before diffreport and a lot of corresponding parameters are involved. Follows are the codes I used for my data. Could somebody give me any suggestion?
datapath = "D:\XCMS_local\neg"
library(xcms)
mzdatafiles <- list.files(datapath, recursive=TRUE, full.names=TRUE)
xset <- xcmsSet(mzdatafiles, method="centWave", snthresh=6, ppm=20, mzdiff = 0.05, prefilter=c(3,500), peakwidth=c(6,120), mzCenterFun="wMean", integrate=1)
idx <- xset@peaks[,"rt"]<3480
xset@peaks <- xset@peaks[idx,]
xset <- group(xset)
xset2 <- retcor(xset, missing=1, extra=1, method="peakgroups", span=0.2, family=c("gaussian", "symmetric"), plottype="mdevden")
xset2 <- group(xset2, bw=5)
xset3 <- fillPeaks(xset2)
reporttab <- diffreport(xset3, "good", "bad", "results", 50, sortpval = TRUE, metlin = 0.15, h=768, w=1024)
Thanks a lot!
Athlon