286
XCMS / Re: Peak filtering
A ppm of 5 as you are using seems quite low. At least my instrument does not perform that good reliably.
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minfrac
minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group
minsamp
minimum number of samples necessary in at least one of the sample groups for it to be a valid group
first_scan=c()
for (i in 1:length(files)){
first_scan[i] = min(xcmsRaw(files[i])@scantime)
}
hist(first_scan)
> temp = xcmsSet(file, lockMassFreq=TRUE)
20111213-001:
Error in if (length(by) && by == 0 && length(del) && del == 0) return(from) :
missing value where TRUE/FALSE needed
> traceback()
11: seq.default(from = start, to = length(object@scanindex), by = freq)
10: seq(from = start, to = length(object@scanindex), by = freq)
9: makeacqNum(object, freqLock, start)
8: makeacqNum(object, freqLock, start)
7: AutoLockMass(lcraw)
6: AutoLockMass(lcraw)
5: do.call(type, list(object, lockMass))
4: .local(object, lockMass, ...)
3: stitch(lcraw, AutoLockMass(lcraw))
2: stitch(lcraw, AutoLockMass(lcraw))
1: xcmsSet(file, lockMassFreq = TRUE)