Re: Peak filling - an example of strange results
Reply #1 –
I would start by troubleshooting the group step. It can be either the m/z or the rt dimension that goes wrong. If the peaks have long tails or your parameters are bad the peaks could get cut up. Or you could have small peaks you don't see without zooming specifically.
It would be easier if you posted parameters for your processing.
You can possibly use a function I have written to understand better what is going on: http://www.metabolomics-forum.com/index.php?topic=577.msg1789#msg1789
Another problem with orbitrap data is that you can get so-called shoulder peaks or satellite peaks in the m/z dimension. If you are affected by that (look at the mass peak and zoom at low intensity around the peak. Do you see some very small noise-like mass peaks around the real peak?) you can use xcmsRaw.orbifilter from https://github.com/stanstrup/chemhelper to filter the raw data before analysis. But I don't think it is that. that usually creates a lot of peaks in the table with slightly different masses.
It looks strange that you say there is a peak at 140 s and the closest it finds is 130 sec...
I am not sure what output table you are talking about. What function generates it? If you use the one that calculates statistics I think it is ordered by p-value (not sure, never use it).