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MAGIC Tool is a Java-based Windows application whose purpose is to help you analyze DNA microarray TIFF files and process comparative hybridization data (glass chips) and Affymetrix information.Portable running modeYou can take advantage of the fact that the tool comes in a portable package and deploy it directly on your computer without having to go through an installation process. Plus, your Windows registry doesn’t get bloated with unnecessary entries. You can store it on any USB flash drive or other devices and take it you. User interfaceMAGIC Tool adopts a clean layout that lets you add files in the working environment using the built-in browse button (there’s no support for drag-and-drop). You can preview the content of the file, explore it using the zoom in and out functions, fit the image to the screen, set the top left and right spots, specify the bottom row, as well as adjust the number of rows and columns. Defining new projectsThe application makes use of projects for storing details and configuration settings about the imported data and performed calculations. Projects can be saved and added for future editing tasks. You can import items with different file formats (TXT, JPEG, TIF, GIF, GRID, INFO or FLAG), add the content of an entire folder, insert files in the project folder and update the project (the adjustments are automatically applied), as well as load the red and green TIFF image pairs. Additionally, you can load the gene list and create a new grid or add a saved one. When it comes to grid creation, you can enter the total number of grids in the TIFF file, specify the spot orientation within the grids (horizontally or vertically), adjust the contrast to help illuminate faint spots, center current grid, enter grid location information using three clicks (setting top left and right spots, and bottom row), adjust the grid to center spots, create multiple grids, and flag problematic spots (optionally). Distinguish signal from noise, generate a series of clusters and moreMAGIC Tool gives you the possibility to distinguish signal from background and generate expression file. You can choose between different methods for distinguishing signal from background, namely fixed or adaptive circle, seeded region growing option (designed for finding the signal for each spot based on the distribution of the signal), or ratio methods (red foreground and background or green foreground and background in order to determine the ratio for each feature on the microarray). What’s more, you can repeat several steps for experimental conditions in your study, manipulate data (transform, normalize, limit data, filter or scramble), add gene info to expression file, filter your data by removing unnecessary genes, calculate dissimilarities (by measuring the differences between every pair of gene expression patterns), generate a series of clusters, build up a list of tasks to be performed in sequence, and compare the consequences of different choices for quantifying, comparing and clustering the same raw dataset . Bottom lineAll in all, MAGIC Tool proves to be a reliable tool that can be used as a powerful educational instrument for helping students explore and process DNA microarray TIFF files. Reviewed by Ana Marculescu, last updated on October 20th, 2014

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