XCMS ret.cor plotting

February 19, 2013, 04:06:32 AM

Dear All,

I found some difficulties with plotting correlation of retention times. I'm using R v. 2.15.1 (x64) and XCMS package release 2.11 (Win7 64bit platform). I usually building the xcmsSet by these rules:

xset=xcmsSet(method="matchedFilter", fwhm=10, snthresh=10, nSlaves=4)
xset = group(xset, bw = 4, minfrac = 0.5, mzwid = 0.025, sleep = 0)

and than I use this script for plotting retention time corrections and plot them in the pdf:

pdf("RetTimeCorr.pdf",w=20,h=18)
xset2 = retcor(xset,missing = 1, extra = 1, smooth = c("loess", "linear"), family=c("gaussian", "symmetric"), plottype="mdevden", span=.02,col = NULL, ty = NULL)
dev.off()

My analyses in this case were 37 minutes long and as you can see in the picture below not all deviations are shown. And I need to see all deviations through whole chromatogram.

Could you pleas help with this problem ??

Thank you

Lukas

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