What's new in Delta2D 4.3

More convenience in quality control and statistical tests

Delta2D 4.3 makes using statistical methods for quality control and expression analysis easier than ever before. The pre-defined sample clusters group images by sample, replicate, or original gel. This makes it easier to apply the methods in the statistics tool to assess quality or to find spots with interesting expression profiles.

For example, image clusters can be very useful to visualize the experiment structure with Principal Component Analysis (PCA):

Principal Component Analysis (PCA) for gel images – each point represents one gel image, points are colored by time. The coloring by time point shows no global effect of time on the expression patterns.	The same PCA result with images colored by treatment. Treatment groups are nicely separated, i.e. the treatment seems to have a bigger impact on the proteome than the time has.

Applying statistical tests is also simplified in Delta2D 4.3. The new cluster selection makes it easy to enter the experimental design: the screenshot shows a two-factor ANOVA for control samples and treated samples with three time points each.

Two-factor ANOVA initialization dialog showing cluster selection for the factors
treatment (two levels: control and treated) and time point (three levels: 0 min,
30 min, 60 min).

This new cluster selection is also available for t-Test and one-way ANOVA.

Complete expression profiles for heterogeneous projects: the Connector tool

Valuable information can be extracted by combining 2D gel projects that were run separately with different experimental goals. Image warping remains the principal tool to compensate for running differences between gels. However, when you want to combine separate experiments that were run with different batches of chemicals or with a long time in-between projects, warping can be a real challenge for some spots.

For those projects, we introduce the Connector tool. It allows for connecting spots directly, independently of the warping. Each connection leads to a matching of those spots which allows for complete expression profiles even over heterogeneous projects.

Matching spots using the new Connector tool.

Easier sharing with import and export of analysis projects

You would like to merge your projects with those of your colleagues? Or would you like to send a project to a collaborator who wants to continue or review your analysis? No problem, with Delta2D 4.3 you can import and export analysis projects easily.

Improved quality of automatic warping

Part of an overlay of two gel images
1) raw overlay
2) with match vectors – unwarped view
3) with match vectors – warped view.

In 2000, DECODON introduced image warping for two-dimensional gels to the market. Since then, we have not only developed automatic image warping to speed up your analyses but also continuously improved the algorithm. With Delta2D 4.3, we now present the next generation of our high quality warping: SmartVectors™ HQ 2.0. This new algorithm allows for high-performance automatic alignment to compensate for running differences between gels.

Other improvements

For every new version of Delta2D, we implement improvements based on valuable feedback from our customers. Here is a partial list for Delta2D 4.3:

• Faster spot transfer Spots can be transferred to multiple images in parallel, taking advantage of multicore processors.
• Gel-image visibility settings are now saved.
• Contrast settings for gel images are applied automatically upon image import.
• Added a button for auto-contrast to toolbar and histogram dialog.
• Improved formatting of web reports, spot album can now also be invoked for selected spots.
• Quantitation tables now show a column 'p value' instead of 't-Test'. The previous 't-Test' column showed (1-p)*100%.