hi,
i am using a UPLC Q-TOF instrument.
i successfully ran the low energy data set using the xcms R package. but once i moved to the high energy data sit, the program shows an error in the retcor step.
my code is:
library(xcms)
tam <- xcmsSet(method="centWave", ppm=20, peakwidth=c(5,20), prefilter=c(3,15), snthresh=10, integrate=1, mzdiff=-0.001)
tam = group(tam, bw = 5, mzwid = 0.06, minsamp = 1)
tam_corr = retcor(tam, method = "loess", plottype = "none", missing = 5, extra = 2)
tam_corr = group(tam_corr, bw = 4, mzwid = 0.06, minsamp = 1)
tam_corr = fillPeaks(tam_corr)
diffreport(tam_corr, 'cont3', 'cont9', 'tam_centWave_Neg_20ppm', sortpval = TRUE, 200, metlin = -0.05)
the program run the first two commands successfully. but once it get to the retcor it have an error message:
> tam_corr = retcor(tam, method = "loess", plottype = "none", missing = 5, extra = 2)
Error in .local(object, ...) :
No peak groups found for retention time correction
could someone tell me why?
thanks,
Topic: high energy data sit problems