2DE Gel Experiments: Project Setup with Delta2D
In a series of four webinars our recommended workflow for analysing 2D gel experiments will be explained. The first step of an analysis is to properly implement the project structure.
For this reason the next webinar
DECODON Academy Webinar
Project setup with Delta2D
is focused on:
- Create a new project; consider backups!
Giving a project a telling name, accompanied by a short description, avoids confusion in a growing number of projects.
- Define groups for replicates.
Statistical analysis is worth if results have a certain significance. Significance increases with the number of (well reproduced) replicates of the same sample. These could be biological or technical replicates.
- Import images, apply basic transformations, assign them to groups.
Orientation of images, contrast settings, optimal usage of the dynamic range, and filtering speckles should be considered when importing the images.
- Use the Project Report to document your setup.
Show a report for your project to document the structure of your experiment.
- Set parameters for multiplex approaches using an internal standard.
Using an internal standard is a well published approach. It is based on dyes which can be used for multiplexing, e.g. the Refraction-2D dyes. Positive effects on image warping and normalization of spot volumes increase the reliability of the results.