Chapter 1
Strategy for Analyzing Gel Images with Delta2D

This chapter provides a short description of Delta2D's approach to analyze the 2DE gel images.

In a nutshell, the typical workflow for creating complete expression profiles and for identifying the interesting ones contains the following steps:

Setup Project

To keep the experimental data handy, we recommend to create a new data pool for every new experimental context. Create a new Project and open the Light Table to include the relevant images and to arrange them in groups in accordance with your experimental setup. More details: section 3.1.

Setup Gel Image Warping

Assign the appropriate Warping Strategy to your project. Using the Warping Setup window you make sure to obtain persistent warping chains and do not produce warping cycles. From a set of prepared strategies choose the strategy that helps to warp images along their similarity. More details: section 3.2

Create Direct Warpings

Examine the gel image pairs with Direct Warp Links one by one and correct them where necessary. More details: section 3.3.

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Note:

Years ago (in 2003) DECODON has introduced complete expression profiles to avoid missing values in the Quantitation Table and the resulting problems during statistical analysis.

Read more about the benefits of 100% Spot Matching at www.decodon.com/Solutions/Delta2D/100_Percent_Spot_Matching.html.

Create the Consensus Spot Pattern

Create a fused image over the complete project using Union as fusion type to get an image that includes every spot existing on any gel image in the project. Detect the spots on the fused image and edit them if necessary. Transfer the consensus spot pattern to all other gel images, and you will receive Complete Expression Profiles that enable reliable statistical analysis by avoiding missing spot quantities as they usually result from individual spot patterns on different images. More details: section 3.4

Analyze Expression Profiles

Open Quantitation Table to view the quantities of all spots. Sort and/or filter the tables for finding interesting expression profiles. Perform statistical analysis to employ a variety of advanced methods for finding patterns in your data, or for clustering your expression profiles. More details: section 3.5.

Present Results

Open the Reports and get an overview on the project or on the interesting expression profiles. Export your data to Powerpoint^TM or Excel^TM. More details: section 3.6.

The workflow as described above is supported by the Workflow window. This window supports your analysis step-by-step by

guiding

you through the different tasks, and

informing

you about the current status of these tasks.

Depending on the actual status of your project, the Workflow window offers links to the required actions.

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Note:

Delta2D is able to completey and reliably analyse DIGE projects. Even for DIGE projects Delta2D's core technologies are quite useful: If you want to analyse a DIGE project with several gels e.g. image warping will provide significant time savings and quality improvements.

For analysing DIGE projects you will have to consider that the project needs to be defined as a DIGE project and that for every image the corresponding gel needs to be defined and which of the images of a certain gel contains the internal standard.

Read more about how to set up DIGE projects with Delta2D in section 5.2