I'm looking for clarification on the gap filling by compulsion parameter under the alignment options.
My data (see attached) show a significant effect when this parameter is enabled (top histogram) vs disabled (bottom histogram). My dataset has 60 samples, and I receive a total of approximately 18,000 features before filtering steps.
Section 2.3.6 of the official docs https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial.html gives the following:
- The "average peak width of samples" is the average FWHM of all detected peaks across all samples within one feature. Correct?
- How does having an average FWHM enable finding peaks with no local maxima?
- How does this parameter cause such a large difference in the number of non-zero values for each feature?
- Based on the parameter "by compulsion" it makes sense that there should be no zero values at all with this parameter enabled, but I still have some (top histogram). Why is that?
An explanation of the parameter algorithm would answer these questions.
Also, reading this prior post (http://www.metabolomics-forum.com/index.php?topic=1469.0) did not answer my questions.
Hi. I untick the "gap filling by compulsion", but the result file is the same with the one with gap filling. I am so confused how I can cancel the gap filling.
I suggest you visit this area of the forum, where Hiroshi has explained and other users have discussed gap filling and it's effect etc. - http://www.metabolomics-forum.com/index.php?topic=1469.0