Johannes Rainer

well, it will be a quite busy plot. it will take quite a while and I think the lower part will be just black. The upper part will actually be...

Yes, good point. I'll add a check based on the number of spectra and m/z values. OK, m/z it will be.

well, yes, but in the `Spectra` package.

I quite don't understand what exactly you want to do, but exporting the data with `write.table` is not what you should aim for - that function simply calls `as.character` on...

Thanks for the clarification. Ideally, you should be able to everything you want to do in R - without the need for import/export. To explain: the `MChromatograms` (or then the...

> Does the "rows" column in the output of chromPeaks refer to the rows in the precursorMz output? yes. The "row" column should be equivalent to the number of chromatograms/transitions...

Please check what data type `precursorMz(cp)` returns. Could be that the lower and upper m/z are reported for precursor and product m/z (note that even if you provide a single...

Yes, exactly, they will be identical if a single m/z value was available (i.e. a target precursor m/z and not a m/z range). To solve your problem I assume you...

Re `QuantitationParams` class. In `xcms` I am using parameter classes to switch between analysis methods (such as `CentWaveParam`, `ObiwarpParam` etc). I think that works nicely, especially because I can put...

Problem is that the *quantification* in xcms is a multi-step approach: 1) chromatographic peak detection (within each sample): `findChromPeak`. 2) alignment (retention time adjustment between samples): `adjustRtime` 3) correspondence (grouping...