Johannes Rainer

@gmhhope no, I don't have a use case or example workflow. But the alignment algorithms in `xcms` do the alignment by default always only on the MS1 data and MSn...

This will unfortunately happen for m/z with a lot of background noise. the noise estimation in `xcms` uses the signal from ~ the same m/z not part of the peak....

There are some issues with *gaps* in retention times in xcms-obiwarp. Some of the problems should have fixed in the more recent version of `xcms` (3.10.1, which can be installed...

honestly, I have no idea whatsoever on this type of data. Eventually @sneumann has some insights?

Uh, this is a really old version of `xcms`. Could you please check if you get the same error with the current version of `xcms` (3.10.2)?

Hm, strange. Could you eventually provide one or two files (or a subset of that) for which this happens so that I could check that locally and fix?

Firstly, I would appreciate if you could use the *newer* functions instead of the `xcmsSet` call - please have a look at the [vignette](https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html). The new functions build directly on...

Very good point indeed @stanstrup ! `xcms` considers all spectra in the peak detection - it does not discriminate between pos and neg polarity. This might indeed be the reaason...

Uh, that sounds like a weird bug. Without actually looking at the data it is pretty difficult to understand what's happening. If possible it would be cool to get a...

amazing! that's a lot of commits! There might indeed be some difficulties merging that, since the _devel_ branch has now become the sort of _master_ that is in sync with...