Frequently Asked Questions

We have collected here the most common questions regarding Delta2D, its features, benefits and function. If you can't find your question here, don't hesitate to send us an email at info@decodon.com or contact us in another way.

1. What is Delta2D?
2. What advantages does Delta2D have over traditional packages for 2D gel analysis?
3. So, what does Delta2D do that I don't get with my present 2D gel analysis package?
4. Can I use Delta2D to analyze DIGE experiments?
5. Can I use Delta2D to analyze 1D gels?
6. I have downloaded the evaluation version. What's next?
7. What's different in the evaluation version?
8. What scanners and file formats are supported by Delta2D?
9. What automatic spot picking / spot cutting robots are supported?
10. I have downloaded and evaluated a previous version of Delta2D. What's new?
11. How can I transfer spot boundaries from one gel to another?
12. Why are spots shifted when exported from one and imported to another gel?
13. How does Delta2D compute the statistical measures (mean, rsd etc.) shown in the statistics table?
14. Can I tell Delta2D to use a proxy for license- or update requests?
15. Why is Delta2D so slow when working with large projects?
16. How do I register the full version of Delta2D?

What is Delta2D?

Delta2D is a software for rapid and reliable analysis of 2D electrophoresis gels. It employs breakthrough image processing technologies that have been under continuous development since 2000. For more information about Delta2D please refer to the Delta2D product page. For an overview of what's new in the current version, see the release notes.

What advantages does Delta2D have over traditional packages for 2D gel analysis?

Delta2D is faster. With Delta2D, you'll only need a fraction of the time you spend with traditional packages. With SmartVectors Technology, Delta2D mimimizes the time needed for matching gel images to each other. Delta2D's approach leads to 100% spot matching, so that the time consuming manual editing of spot matching is obsolete. Spot detection and editing is only done for the fusion image, as opposed to each image. For a 24 gel experiment this means you only have to check and correct one set of spot boundaries, as opposed to 24 different sets.

Delta2D produces more reliable results. With Delta2D's 100% spot matching you get complete expression profiles for every protein. Besides higher throughput, this leads to significantly improved statistical confidence, so you can, for example, identify more biomarker candidates from the same experiment. Throughout the analysis, Delta2D gives you opportunities to do cross-checking, e.g. dual channel images to assess the warping, or direct display of the spot background image to assess quantitation.

Delta2D lets you do more with your data. For example, Delta2D's Protome Maps give you a high-level view on a whole experiment. You can make maps that contain all identified proteins, color code them to show protein properties such as isoelectric point and molecular weight, highlight proteins with specific expression patterns, and more. Getting data out of Delta2D is easy — use the convenient exports to Excel, PowerPoint, and Text (CSV), or use the raw analysis results in Delta2D's open XML format.

Delta2D is suitable for all types of 2D gel setups. You can analyze classical experiments as well as DIGE (Fluorescence 2D Difference Gel Electrophoresis) and other multiplex experiments using the same application.

So, what does Delta2D do that I don't get with my present 2D gel analysis package?

Of course, that depends on what your present software is. Contact us for an in-depth answer. Here is a partial list of Delta2D's features that are not available in most of the competing packages:

• An approach to spot matching based on image fusion and warping that eliminates matching problems. This is unique in Delta2D and one of the main reasons for higher productivity and reliability of results.
  
• Analysis of classical (single stain), DIGE and other multiplex experiments in one package.
  
• Great, fast qualitative image comparison based on whole image warping and dual channel images.
• Background subtraction based on whole image data. Unique in Delta2D.
• PowerPoint export where every label and spot is a real PowerPoint object that you can modify on the slide / poster.
• Image fusion for producing average images and proteome maps. Unique in Delta2D.
• Labels that do not get deleted when you edit a spot  (a problem in many other packages).
• Labels that can be transferred to / from a proteome map using the warping (packages without precision warping cannot do this).
• An approach to spot editing that is very reproducible. Delta2D uses minimal manual input, e.g. you click where you want to split a spot, as opposed to free-hand spot 'drawing', 'trimming', and 'erasing' in other packages. Unique in Delta2D.
• Compatibility with image formats (esp. calibration) of the whole Fuji FLA line, including the new FLA 5100
• Scouts that integrate protein information from web-based resources directly on the gel
  
• Spot color coding according to expression profiles (e.g. a proteome map where we compare three different conditions). Unique in Delta2D.
• Label color coding according to e.g. pI and Mw. Unique in Delta2D.
• Seamless integration with our proteomics information system Protecs
• Active development by a committed vendor with major upgrades every year.

Can I use Delta2D to analyze DIGE experiments?

Yes. Delta2D supports electrophoresis technologies that generate multiple images per gel. One of these is DIGE (Fluorescence 2D Difference Gel Electrophoresis), where multiple samples are labelled using different fluorescence stains and then comigrating on a single gel. For DIGE experiments, Delta2D supports all experimental setups, including those using an internal standard.

See Differential in gel electrophoresis (DIGE) - image analysis with Delta2D for more information.

Can I use Delta2D to analyze 1D gels?

It depends. Delta2D was developed and optimized for 2D gels. One-dimensional gels have different spot forms so you might have to use the spot editing more extensively. If the order of the lanes does not change between your gels, you can use Delta2D's warping to align different gels and produce expression profiles the way you would for 2D gels. In general, you'll probably be better served by a software package that is specifically developed for 1D gels, such as LabImage 1D.

I have downloaded the evaluation version. What's next?

Immediately after you have completed the download, you'll receive an automated email response with a license file that is valid for 3 days. You'll need this file in order to be able to use the evaluation version.

For an introduction to Delta2D, please consult the Quick Guide from the Getting Started section in our documentation area. The guide will show you how to setup an analysis project and walk you through your first analysis session.

What's different in the evaluation version?

Delta2D evaluation version differs from the full version in two ways:

• It is not possible to save or export data produced by Delta2D in any way.
• Image files are overlaid with water-marks.

What scanners and file formats are supported by Delta2D?

Delta2D supports virtually all scanners in use today, incuding devices made by Fuji, GE Healthcare (formerly Amersham), and Molecular Dynamics. Supported file formats include TIFF (8, 12, and 16 bit), PNG, JPEG, BMP as well as vendor-specific formats like IMG, or GEL. See our Scanning Guide for more information about image file formats in general.

What automatic spot picking / spot cutting robots are supported?

Delta2D supports these devices:

• Genomic Solutions ProPic
• PerkinElmer ProXCISION
• Molecular Dynamics devices
• GE Healthcare Ettan Spot Handling Workstation
• Bruker Proteineer line
• Bio-Rad Exquest Spot Cutter

Additionally, a generic format is offered which you can transform to control files for other devices. If a customer's device is not listed above, we'll usually create the necessary capabilities for free. The only condition for this is that the maker of the device makes available the specification of the devices pick list format.

I have downloaded and evaluated a previous version of Delta2D. What's new?

See the latest 'What's new in Delta2D' and release notes on our Delta2D Documentation page.

How can I transfer spot boundaries from one gel to another?

To transfer spots, right click on the thumbnail of the gel in the Project Manager which contains the spots you want to transfer, and choose Transfer Spots to Gel from the context menu. You will be able to choose your target gels in the context menu.

Please note: Since warping informations between gel images are necessary for transferring spots from one gel image to one or more others, it only works within a project and between gel images with valid warping informations.

Why are spots shifted when exported from one and imported to another gel?

The function of exporting and importing spot boundaries is meant only for two main purposes:

1. Having the possibility to make detailed snapshots of spot detection with different or certain parameters
and
2. Having the possibility to exchange single gels and / or their data with other users without the necessity of copying the complete pool.

This presumes that spot boundaries belong to the image they were detected on. Thus it is not necessary and for the aspect of reproducibility even not wanted to consider warping to any other gel image when importing spots. If you want to transfer spots from one image to another, you can use the feature "Transfer Spots", available from the context menu of the image thumbnails in the Project Manager.

How does Delta2D compute the statistical measures (mean, rsd etc.) shown in the statistics table?

Let's start with the mean. It is computed for every replicate group, using the relative volumes of the spots in a group. The formula for the mean is

The relative standard deviation is shown in the column rsd, in percent. The absolute standard deviation is a measure of the spread of sample values, it is defined as

The relative standard deviation (rsd) is computed by normalizing the standard deviation with the mean, and then multiplying by 100 to get a percentage value:

The median is defined such that at most half the spots in the group have values less than the median and at most half have values greater than the median. It is computed by sorting the intensities and then taking the middle one (if the number of spots is odd), or the average of the two middle ones (if there is an even number of spots). So, if

are the sorted spot quantities then the median is defined as

Ratios are computed according to the setting at the top of the quantitation table. By default, it is the quotient of the group means of relative spot volumes. The denominator of the ratio is always taken from the first group displayed in the project manager. Hold the mouse pointer over the ratio column heading, the tooltip will show details about the ratio computation. You can have the ratio is displayed in terms of fold change, where negative values mean decreases. For example, a fold change of -3 means a threefold decrease. To switch between normal and fold change display, go to the Preferences dialog and use the "Show Ratio of Spots as Fold Change" checkbox.

Delta2D computes t-Test values for certain pairs of replicate groups. The test is a paired two-sided Student's t-Test, with the assumptions of equal unknown variance and unpaired samples. The null hypothesis is that both groups have equal means. Delta2D computes the p-value, which is the probability that a test statistic at least as significant as the one observed would be obtained assuming that the null hypothesis were true (i.e. the differences in quantities are the result of mere chance). The value q shown in the statistics table is derived from the p-value as follows:

So higher values mean a higher probability that the null hypothesis is false. The value q is the t-Test value shown for the paired test applied to every group vs. the first one displayed in the project manager.

Can I tell Delta2D to use a proxy for license- or update requests?

Delta2D needs to contact our web server for two possible reasons:

1. to validate special, so called 'web checked' licenses and
2. to check for updates

If your network situation demands to set your internet browser to use a proxy, then Delta2D very likely will need the same settings, otherwise you will see error messages saying that the license server or the update server could not be connected.

Just follow these steps to set a proxy in Delta2D:

• locate your Delta2D installation folder, on Windows something like "C:\Program Files\DECODON\Delta2D\3.6"
• Open the file "Delta2D.vmoptions" you can find there with any text editor
• add the following line(s) at the bottom:

  -Dhttp.proxyHost=proxyhost
  -Dhttp.proxyPort=portNumber
  

  where you specify proxyhost (resp. portNumber). The second line is optional and only necessary if the proxy port is other than 80.
• Save the file and start Delta2D

Why is Delta2D so slow when working with large projects?

Probably you need to adapt Delta2D's memory settings: open the preferences dialog (in the project manager, go to Project / Preferences), change to the Memory tab and click on 'Recommend' or 'Recommend (Nice)'.

How do I register the full version of Delta2D?

Background information: The single-machine version of Delta2D is copy-protected by a license file that is specific to you and your computer. Initially, you get a generic license file. Registering a license gives us the information we need to make a specific license file for your computer.

• After installation, please start Delta2D. You will be prompted for a license file. Please click on the "Import" button and select the license file you either found on your cd, received by e-mail or downloaded from your private download area.
• The dialog now shows a button "Register". Please click on the button and follow the instructions to send us your registration request by email. The registration request contains an identification code for your computer. Meanwhile you can start using Delta2D in Demo mode.
• We will process your request and send you the valid registration key, or a new license file corresponding to your computer.
• (Re-)Start Delta2D to obtain the registration dialog again and complete the registration with the registration key or the registered license file we sent by email.
  • Option 1: you received a license key. A license key looks like this: FXWEH-WJVXQ-XPQ5H-HWFEB-JSFBW-XYFLN-NBMWX-5XY4U-9WMJ7
    In the licensing dialog, click on the button "Enter license key". Copy the license key from your e-mail into the dialog and press OK.
  • Option 2: you received a license file. The license file ("registered license file") contains a key that is specific to your computer. Please save the file from your e-mail to some place on your computer. In the Delta2 registration dialog, click on "Import license file" and select the license file.
• Now your copy of Delta2D is fully licensed and operates in full mode.