I have downloaded XCMS to use it on my chromatograms. I have converted them to .mzXML files using OpenChrom and I write the following in R (after loading the xcms library) and the following error:
> f = list.files("C:/Users/Aris/Documents/filter", recursive = TRUE,
> full.names = TRUE)
> xset <- xcmsSet(f)
C01_B_inj1: Error in seq.default(floor(mrange[1]/step) * step,
ceiling(mrange[2]/step) * :
invalid (to - from)/by in seq(.)
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
>
>traceback()
11: stop("invalid (to - from)/by in seq(.)")
10: seq.default(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) *
step, by = step)
9: seq(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) * step,
by = step)
8: .local(object, ...)
7: findPeaks.matchedFilter(<S4 object of class "xcmsRaw">)
6: findPeaks.matchedFilter(<S4 object of class "xcmsRaw">)
5: do.call(method, list(object, ...))
4: .local(object, ...)
3: findPeaks(lcraw, ...)
2: findPeaks(lcraw, ...)
1: xcmsSet(f)
>
Note: C01_B_inj1 is the name of the first chromatogram.
Does anyone know if this error has to do with my files or with how I generated the .mzXML files? Should I determine specific parameters or pre-process my data?
Thank you for your time time and concern.
What kind of instrument are you using? Are you sure the files converted OK ?
Have your tried converting them using proteoWizard (http://https://xcmsonline.scripps.edu/docs/fileformats.html) ?
Can you try loading a single file and post the output of
xr <- xcmsRaw("C:/Users/Aris/Documents/filter/C01_B_inj1.cdf") ## replace .cdf with whatever the actual file extension is
xr
The instrument is the a Varian Saturn 2200 and the files are .sms.I am not able to upload and attach a chromatogram file in this forum.
I have also installed proteoWizard but it does not recognize the sms files.
Openchrom has expired and I am not able to use it anymore. Are you aware of any other reliable software converting MS files?
This code does the task you are asking about. http://http://www.members.optushome.com.au/david.a58/msutils.html
Sorry about the late reply, but I have not been here for a while.