Any possible info about a retcor error?
Dear xcms developers,
I would like to ask (I know it is a quite general question though...) what might be causing the following errors (not at the same time but using different parameters) in a 2nd pass of retcor after a first data grouping:
Error in stepfun(rtcor[[i]][-1] - diff(rtcor[[i]])/2, rtcor[[i]] - rtdevsmo[[i]]) :
stepfun: 'x' must be ordered increasingly
Error in quantile.default(abs(rtdevsmo[[i]]), 0.9) :
missing values and NaN's not allowed if 'na.rm' is FALSE
I am trying to process 75 samples of CE/MS data in netcdf format, after filtering out 2 time intervals from the beginning and the end of the scan range. I know that xcms was not initially developed for CE/MS data but it has been sucesfully used in a couple of publications. I should mention that these errors occur in any (steps, snthresh) configuration (matchedFilter), other than the default (steps=1, snthresh=10). For example I have tried (steps=1, snthresh=7), (steps=3, snthresh=10), (steps=3, snthresh=7), (steps=2, snthresh=7) and (steps=2, snthresh=10) is currently running. I am using sigma=7 (found to be good for my data after some visual inspection). The errors are always occuring in an iterative grouping/rt correction procedure, on the 2nd iteration (initial grouping bw=30 or 50, next values 30 or 20). The parameter steps=3 was suggested in a publication using xcms with CE/MS data.
These errors was not occuring in the previous xcms version I had on my system (1.23.1), when using several parameter sets like the above. Thanks in advacne for any replies!
Panos
Topic: Any possible info about a retcor error?