Regatta/User Guide/Best Practices

From Bawiki

Up: Regatta/User_Guide Back: Regatta/User Guide/Reference Guide Next: Regatta/User Guide/Appendices

---

Contents 1 Usability Tips 2 General Advice 2.1 Regarding .trawl files 2.1.1 Reconciling trawls from many models 3 For quantitative analysis 3.1 Normalizing your lists 3.2 Use Coefficients of Variation Filtering

Usability Tips

• List labels may be edited only when the list is not displayed.
• The Active Workspace is sortable by list label or type.
• Large files load slowly due to data table and plot graphics creation.
• You may create your own trawl-type data files using Excel or Notepad with the ProTrawler CSV Format or the Regatta CSV Format and benefit from Regatta without having used ProTrawler. (But using ProTrawler is easier.)

General Advice

Regarding .trawl files

Reconciling trawls from many models

If you've trawled a chromatogram using many models, then this advice will help reduce the several model files to one usable file.

1. Load the trawl files.
2. Highlight the files.
3. Select the Reconcile Method from the Methods Tab.
4. Press the Reconcile button.

For more on what actually happens, see Algorithms/Reconcile.

For quantitative analysis

Normalizing your lists

Whenever you first load .trawl files, don't forget to normalize them. We find that sum normalization works best for biomarker discovery projects, especially if you anticipate using a quantitative method like PCAs or |CVs.

Use Coefficients of Variation Filtering

For biomarker discovery projects that rely on quantitation, e.g., up-down regulation, use Coefficients of Variation Filtering after normalization and before PCAs.