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?