Vendors of microarray chips provide software tailored for their products. There are also various packages in R for analyzing microarray data. Likewise, JMP, or at least JMP Genomics, has procedures for analysis of microarray data. As with any software, the choice depends upon a number of factors, including how well it meets your needs, availability for your operating system and hardware, quality and accessibility of technical support, and cost. R has the advantage of being free and cross-platform, but it can be difficult to learn. JMP and JMP Genomics are expensive, but easy to use and backed by excellent technical support.

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