Metabolomics Society Forum

Software => MS-DIAL => Topic started by: benton_anderson on December 28, 2021, 10:48:58 AM

Title: Clarify gap filling by compulsion parameter
Post by: benton_anderson on December 28, 2021, 10:48:58 AM
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:

Quote
If you check this, the peak recognition is performed by the average peak width of samples having the metabolite feature even though no local maximum is observed in the chromatogram. This is validated by default.


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. 
Title: Re: Clarify gap filling by compulsion parameter
Post by: Dongfang on November 03, 2022, 06:55:27 AM
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.
Title: Re: Clarify gap filling by compulsion parameter
Post by: agentfourtea7 on November 17, 2022, 04:30:29 AM
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