Thank you for your reply. Unfortunately, I don't have any experience with R. I will look into finding other people around here who might know R better. I will try to contact you back when I can find someone. Thank you.
I have generated some MRM data from Agilent QQQ LC/MS. I thought it would be useful to get the peak area for all of the peaks at once. Is MRM data supported by xcms? I have tried to use xcmsSet(), but it gave me the following messages:
> xs <- xcmsSet() 2_110927pos_wc-ptc1a: 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()
I guess this is understandable, since the files contain mainly MS2 data, and not MS1. Is there any way around this problem using xcmsSet()?
