Skip to main content ↑ ↓
Topic: zero intensity after diffreport (Read 4841 times) previous topic - next topic

zero intensity after diffreport

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?

Code: [Select]
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

Re: zero intensity after diffreport

Reply #1 –
One thing that jumps at me is that you are aligning TOF data with a parameter setting for single quad (mzwid = 0.25 is default for group).

Re: zero intensity after diffreport

Reply #2 –
Hi, Ralf,

Thanks a lot for your answer.

Quote from: "Ralf"
One thing that jumps at me is that you are aligning TOF data with a parameter setting for single quad (mzwid = 0.25 is default for group).

To my best understanding, there's a false setting for the parameters used in group function. How large is the proper mz width for TOF data? In XCMSOnline, 0.05 is the default for q-TOF data. I'll try this value first.

Thanks a lot again!

Regards,

Athlon