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TM4 Microarray Software Suite
Microarray analyses of gene expression are incredibly useful because they generate a large amount of data. They are also somewhat of a hassle to deal with because, well, they generate a large amount of data. Thankfully, researchers at the Dana-Farber Cancer Institute are here to help us all out with TM4, a microarray software suite composed of (yes, you guessed it) four separate programs related to the collection and analysis of microarray data. And yes, all four programs are free to download. They include: MADAM (Microarray Data Manager, to load/retrieve data to and from a database), TIGR Spotfinder (for image processing), TIGR MIDAS (Microarray Data Analysis System, to process/normalize raw experimental data), and MeV (MultiExperiment Viewer, to analyze and identify gene-expression patterns). My only complaint is that MADAM only runs on Windows. The others are compatible with Windows-, Linux-, or Mac-based operating systems.