Johannes Rainer

Ah, yes, sorry, my fault `ref = "jomaster"` is correct. I misspelled it in the original message.

If you use the same 15 pooled samples for the subset-based alignment in the first and second (including only blank samples) you should get the same number of *peak groups*....

I could try to tune some examples and unit tests even more.

With the `chromatogram` function you want to extract an ion chromatogram from the data. It makes only sense to extract such a chromatogram from either MS1 data or MS2 data,...

We haven't integrated warpgroup into `xcms`. To me that sounds like an interesting idea and contributions in the form of pull requests are anyway highly welcome! (@sneumann any comments?).

General info about `attempt to select less than one element in OneIndex` errors. These occur mostly if you run parallel processing and the system (or R) runs out of memory....

Instead of opening all filehandles at the beginning (note that there might also be a limit of open file handles either in R or the operating system) I would suggest...

Thanks @danagibbon for the very detailed report. First thing I would suggest is to update `xcms` to the most recent version and try again: `devtools::install_github("sneumann/xcms", ref = "RELEASE_3_8")` Note that,...

first of all sorry for the late reply - been pretty busy. *obiwarp* seems to be very fragile depending on the input data... could you please try to run that...

Please note that for MSe data there is another solution: https://github.com/sneumann/xcms/issues/451 You can do first *classical* detection in MS1 and then run a second round of peak detection on MS2...