Johannes Rainer

Honestly, I've no idea. I'm only using the command line version from the docker image. The problem also is that the documentation on the chromatogram filters is pretty scarse.

The developmental `mzR` version with an updated proteowizard code is [available](https://github.com/sneumann/mzR/tree/feature/updatePwiz_3_0_21263). With this version it should be possible to read the mzML files. It might take some time until this...

I'll also chime in here - seems to be a busy issue :) R version 3.4.x should be OK, but you have an outdated version of MSnbase. Please run: ```r...

Thanks @cbroeckl for the benchmark. Interesting, I was not expecting that netCDF is that slow. Just to explain: the initial import of the data with the `onDisk` backend usually is...

Thanks @cbroeckl ! Some benchmarks on the file you provided: ```r library(xcms) library(microbenchmark) cdf

So, basically to read mzML files you would do: ```r sps

Yes, that makes sense. @stanstrup , please open an issue in `Spectra`. Note also that the `chromatogram` function also has `mz` and `rt` parameters and in that we support passing...

Seems that proteowizard (which is used by the `mzR` package to import the data) has a problem with the data. I've never used openchrome for conversion - maybe you try...

Re harmonising: always a good idea. Question is whether we should also harmonize the use of `ggplot` or base plotting. Although `ggplot` is powerful, I'm still a fan of the...

> `plot(, type = "XIC", rt, mz)` - former `plotMsData` (see above) You think parameters `rt` and `mz` are required? We could also drop these leaving the task of subsetting...