Hi all,
I have some problems after the fillPeaks. This is the code I work with:
xset <- xcmsSet(files, method="centWave", snthresh=10, ppm=10, mzdiff=0.01,
prefilter=c(3,500), peakwidth=c(10,60), nSlaves=4)
idx<-which(xset@peaks[,"mz"] > 100 & xset@peaks[,"mz"] < 1000)
xset@peaks<-xset@peaks[idx,]
xsetR <- retcor(xset, method="obiwarp", profStep=0.1, plottype="deviation")
xsetR <- group(xsetR, bw=5, mzwid=0.025, minsamp=5)
xsetF <- fillPeaks(xsetR)
I have this warning message after the fillPeaks step:
There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: In .local(object, ...) :
getPeaks: Peak m/z:397.366577148438-397.368316650391, RT:364.471-378.604is out of retention time range for this sample (/home/cism/Documents/Controllo10.mzXML), using zero intensity value.
2: In .local(object, ...) :
getPeaks: Peak m/z:479.481033325195-479.483581542969, RT:364.471-391.31is out of retention time range for this sample (/home/cism/Documents/Controllo10.mzXML), using zero intensity value.
3: In .local(object, ...) :
getPeaks: Peak m/z:480.484039306641-480.487976074219, RT:364.471-392.215is out of retention time range for this sample (/home/cism/Documents/Controllo10.mzXML), using zero intensity value.
4: In .local(object, ...) :
getPeaks: Peak m/z:610.453125-610.457580566406, RT:364.471-383.212is out of retention time range for this sample (/home/cism/Documents/Controllo10.mzXML), using zero intensity value.
5: In .local(object, ...) :
getPeaks: Peak m/z:617.063537597656-617.069519042969, RT:364.471-376.196is out of retention time range for this sample (/home/cism/Documents/Controllo10.mzXML), using zero intensity value.
6: In .local(object, ...) :
getPeaks: Peak m/z:713.638122558594-713.643371582031, RT:364.471-398.001is out of retention time range for this sample (/home/cism/Documents/Controllo10.mzXML), using zero intensity value.
7: In .local(object, ...) :
getPeaks: Peak m/z:798.143920898438-798.152557373047, RT:364.471-376.5195is out of retention time range for this sample (/home/cism/Documents/Controllo10.mzXML), using zero intensity value.
......
So, I think there is a specific problem, for example, in the file called Controllo10.mzXML, but clustering the RT differences it seems that the groups aren't too different.
minlength <- min(sapply(xsetR@rt$raw, length ))
devs <-
sapply(1:length(xsetR@rt$corrected),
function(x){
(xsetR@rt$raw[[x]]-xsetR@rt$corrected[[x]])[1:minlength]})
colnames(devs) <- sampnames(xsetR)
ddevs <- dist(t(devs))
hdevs <- hclust(ddevs)
x11(); plot(hdevs)
The result of the clustering analysis is:
[attachment=1:29id13si]HCluster.png[/attachment:29id13si]
And this is the result of the retcor step:
[attachment=0:29id13si]RTDev.png[/attachment:29id13si]
Do you have any suggestion to try to solve this kind of problem?? Should I discard from my dataset the sample in the warning message??
Best
Riccardo
P.S. This enormous problem in the RT are due to the use of a HILIC LC column... :evil:
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