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Frequently Asked Questions
| Q: | What is the difference between the two available versions of Melanie 7.0? |
| A: | In addition to the features that are also present in the non-DIGE version, the DIGE version enables you to analyze DIGE experiments. It includes the powerful co-detection algorithm from GE Healthcare's Decyder software and a set of specific tools designed to optimally analyze DIGE experiments. |
| A: | Differential gel electrophoresis (DIGE) is a method for pre-labeling protein samples prior to two-dimensional electrophoresis. By allowing different samples to be run on a single gel, one of which can be an internal standard, it can significantly reduce the problems of inter-gel variations. The system is based upon the use of up to three cyanine dyes possessing unique fluorescent properties. The dyes (Cy2, Cy3 and Cy5) are mass- and charge matched N-hydroxy succinimidyl ester derivatives that differentially attach to lysine residues in a protein. Therefore the labeled proteins migrate simultaneously on the 2-DE gel but still produce distinct excitation and emission spectra. |
| Q: | Can I analyze images from 1-D electrophoresis with Melanie? |
| A: | Melanie has been designed exclusively for 2-DE image analysis. Its detection has not been optimized for the analysis of bands on 1-D gels, and therefore it is not recommended to use the software for 1-D applications. |
| Q: | What are the image file formats supported by Melanie 7? |
| A: | The supported file formats for gel images are MEL (Melanie/ImageMaster format), GEL (Molecular Dynamics), IMG (Fuji), TIFF (Tag Image File Format) and PNG (Portable Network Graphics). |
| Q: | Can I analyze gel images with white spots on a black background? |
| A: | When you have such an image, you must use the "Tools > Gels > Invert Gray Levels" feature in Melanie to invert the gray levels prior to analysis. |
| Q: | What should I do if the gels were scanned in different orientations? |
| A: | It is really important that all your gel images are in the same orientation. The typical orientation for a 2D gel is the following: - acidic end on the left and basic on the right.
- heavy mass on top and lighter on the bottom.
Melanie provides rotation and flip tools to easily correct a wrong orientation when needed. |
| Q: | How many landmarks should I define on my gels before matching? |
| A: | In most cases, very few landmarks are needed to match gels (between 0 and 2). We recommend to choose non ambiguous, small and very well focused spots. |
| Q: | How do I find the most significant expression changes between classes of gels? |
| A: | Melanie offers several possibilities to carry out statistical comparisons between populations of gels. One of the easiest ways is to use the overlap values that are displayed in Inter-Class Reports. First, we recommend to filter the spots according to their Ratio (for instance, you can keep the spots that have a Ratio higher than 2), and then to sort the remaining spots according to their Gap values. Generally, this method gives very good results. Please note that this procedure is illustrated in the tutorials. |
| Q: | Why are some menu options greyed out? |
| A: | Menu options can be greyed out for different reasons. First of all, the DIGE functionalities are greyed out if your license is only valid for the standard package. Second, it is important to remember that most operations can only be carried out if the appropriate objects (gels, spots, annotations, matches, etc.) are selected. Therefore, if a menu item is greyed out, make sure that the objects on which the operation should act are selected. Finally, depending on the context and especially the type of worksheet your work in, certain operations can or cannot be carried out on the opened images (e.g. matching is only possible in a [MatchSet] worksheet). |
| Q: | Where can I find the Physical Address of my computer? |
| A: | - On the computer where the eLicense file should be placed, select "Start >(All) Programs > Accessories > Command Prompt".
- When the command-prompt appears, click on it and enter the command "ipconfig /all" (making sure to leave a space between the ipconfig and the /all).
- Among the displayed information, make a note of the "Physical Address" but without any dashes or colons. If the computer has several physical addresses (there can be one for each network, i.e. Ethernet, card in the computer), any of them can be used for identification. Please verify that the "Physical Address" is correctly noted. Otherwise the license file will not work.
- Close the command-prompt window.
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| Q: | How can I purchase Melanie 7? |
| A: | Melanie can be obtained from GeneBio. To purchase the software, you can contact us here. |
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