Johannes Rainer
Johannes Rainer
Re data set: sorry, I don't know any such data sets. Re pre-processing handling gaps: the *peak groups* alignment should be able to work also with such data sets -...
Do you mean the `ChromPeakAreaParam` gap-filling method for the `fillChromPeaks` function? There is an internal function `xcms:::.features_ms_region` that returns the m/z and retention time regions. It takes the `XCMSnExp` object...
I see. I had a look at the code again and (if I did not get it completely wrong) the `"into"` is calculated as the sum of intensities within `"rtmin"`-`"rtmax"`...
Sounds indeed interesting (as we also now run into similar issues). In theory one would *only* need to add new rows to the `chromPeaks` matrix (and the `chromPeakData` `DataFrame`). I'm...
That is indeed unexpected! I will have a look into it.
Getting closer to the explanation: reading just one file and comparing the content of the data. The `xcmsSet` call reads each file with `xcmsRaw` and performs peak detection on that....
In fact, when the empty spectra are removed from the *new* object the results of centWave are identical: ```r tmp 0] res_new
Good point! Could you briefly describe how such data would look like?
I meant the raw data - is it one mzML file per sample with two retention times per spectrum? I am aiming to use the `MSnExp` or even bettern the...
OK, so this will be something for `mzR` I believe - the representation of the data in `R` shouldn't be too difficult. `xcmsRaw` would have to be tweaked quite considerably,...