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Messages - roager

1
XCMS / Re: Identified features does not match mz values in raw file
I tried to export to mzXML files manually from Bruker's DataAnalysis, thereby not using CompassXport. (The disadvantage is that you can only export one file at a time, so it takes more time compared to CompassXport)

However, by doing so I fixed the problems and got the 'real' mz values after running XCMS.

So the problem is the conversion by the CompassXport program.
3
XCMS / Identified features does not match mz values in raw files
My problem is that the features identified by XCMS are off with around 0.02Da compared to raw files (.d) accessed by Bruker's Data Analysis 4.2.
What could be the explanation for this?

I am using RStudio (Version 0.98.994), XCMS (version 1.38.0).

I have a HPLC-qTOF (Bruker) which produces .d files. I have converted these files into .mzXML files by CompassXport 3.0.

Following I run
Code: [Select]
library(xcms)
xset <- xcmsSet(myDir, ppm = 30, peakwidth = c(10,60), method = "centWave", snthresh = 10, noise=100, prefilter = c(4,1000), 
                mzCenterFun = "wMean", integrate = 1, mzdiff=-0.01, fitgauss = TRUE, profparam = list("step" = 0.01)) 

xset1 <- group(xset, bw = 30, minfrac = 0.5, minsamp = 1, mzwid = 0.025, max = 50)
xset2 <- retcor(xset1, missing = 1, extra = 1, smooth = "loess", span = 0.2, family = "symmetric") 
xset3 <- group(xset2, bw = 30, minfrac = 0.5, minsamp = 1, mzwid = 0.025, max = 50)
xset4 <- fillPeaks.chrom(xset3)
reporttab <- diffreport(xset4, "A", "B", "Outputfile2", 11, metlin = 0.15, h = 480, w = 640)
xset5 <- peakTable(xset4, filebase="name")

Any help is really appreciated!
6
XCMS Online / Problem with uploading .d files
Every time I try to upload .d files it somehow fails. The menu where you select your files and start uploading does work. However, after having uploaded the files, the uploading-window never closes again automatically and 'Storage Quota Usage' is unchanged.

I don't know how I can overcome this problem?

I am using Google Chrome Version 27.0.1453.94 m on a computer with Windows 7. I have the newest Java version installed (Version 7 Update 21).

Thanks for any help,
Henrik