Re: xcms vs xcms online
Reply #3 –
Latest as in stable or development version ?
sessionInfo()
This is how you can find out if you get different numbers of features per sample :
for (i in 1:length(filepaths(xset))) {
cat(basename(filepaths(xset)[i]), length(which(peaks(xset)[,"sample"] == i)), "n")
}
Another thing to compare would be the retention time correction curves.
XCMS Online uses profStepPad() as the profiling method for OBIWarp.