Johannes Rainer

Re correlation of `Chromatograms`, yes, can do that. Regarding the reconstruction - I didn't yet think of the best way. `into` sounds good, but might be nice if we could...

After aligning and correlation we will have a `chromPeaks` matrix containing only the (MS2) peaks for one MS1 chrom peak that pass the correlation criteria. So it should be straight...

Question @michaelwitting : do we expect that the MS2 signal for an ion is higher than the corresponding MS1 signal? The plot below shows the MS1 chromatogram in black (thick...

OK 👍

I see the point @michaelwitting - only that we are processing the data at present separately for each file (to enable parallel processing). What if we add this as a...

Yes, that (annotation for reconstructed spectrum) would/should be doable. If possible I would like to keep the definition of the MS2 spectrum separate from the *quality assessment* of the reconstructed...

So, for each MS1 chrom peak we can get the MS2 chrom peaks with a correlation higher than a certain threshold. From that we can reconstruct the MS2 Spectrum. We...

Summarizing, the `reconstructChromSpectra` is somewhat similar to MS-DIAL's `MS2Dec` function. The `reconstructFeatureSpectra` could in addition support a reconstruction similar to MS-DIAL's `CorrDec` function since we do have then also the...

Could you please provide the output of `sessionInfo()`. Also, it seems that `Rhdf5lib` is the culprit, please try to install it directly with `BiocManager::install("Rhdf5lib")`.

May I suggest to use the *new* functions instead of the deprecated *xcmsSet* code? That will also make it easier for me to find the origin of the problem. Also,...