Johannes Rainer

One possibility would be Bioconductor's `limma` package - although it was developed originally for gene expression (microarray) data it works also good for metabolomics data. You can find the userguide...

Dear Callum, if `rdata` is an `OnDiskMSnExp` object it will still need the original mzML file even if you set `copy = FALSE`. The `OnDiskMSnExp` object uses the *on-disk* mode...

That's good news! `enrichplot` would be great for me!

Sounds great to me! Actually the stuff I put together is more or less just an ugly hack... never done any serious lisp programming before... I'll have a look at...

Can you please provide an output of your `sessionInfo()` and what settings you used for the alignment?

Thanks for the information. Can you try the following: do you get the same error without parallel processing? Call `chromatogram` using `BPPARAM = SerialParam()` (please also add all other parameters/settings...

I'm not familiar with parallel processing on Windows - could maybe also be a firewall issue? Following a bit the discussion [here](https://stackoverflow.com/questions/41639929/r-cannot-makecluster-multinode-due-to-cannot-open-the-connection-error), maybe it helps to provide the hostname of...

Are you sure this is an error related to `xcms`? I don't see which function from `xcms` was actually called to result in this error...

where do you get this output from? this does not look like typical output from R. Also, the message you see is not an error but a warning (*you might...

can you maybe provide some more information on your data? what is it? SWATH? DIA? note that at present this approach _reconstructs_ only fragment spectra (from MS2 chrom peaks) separately...