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XCMS / plotTIC vs plotEIC vs getEIC vs rawEIC
While using the xcms-package I came across about 4 different ways to produce TIC or EIC figures. The figures show different results. Presumably I use the wrong parameter settings, or misunderstand some of the concepts. The example below illustrates my problem:
Code: [Select]
library(xcms)
library(faahKO)
cdfpath <- system.file("cdf", package = "faahKO")
cdffiles <- list.files(cdfpath, recursive = TRUE,full=T)
xr <- xcmsRaw(cdffiles[1])
xr
par(mfrow=c(4,1))
plotTIC(xr)
plotEIC(xr, m=c(200,600), rt=c(2501.4, 4499.8))
t1 <- getEIC(xr, mzrange=cbind(200,600), rtrange=cbind(2501.4, 4499.8))
t2 <- cbind(xr@scantime, rawEIC(xr,mzrange=range(xr@env$mz))$intensity)
plot(t1)
plot(t2, type = "l")
This piece of code leads to the attached figure.
[attachment=0:3lvtgvgp]question.jpeg[/attachment:3lvtgvgp]
Could you help me understand the different outcomes? All help will be very much appreciated!
Kind regards, Hans
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