Microarray Analysis Tools

Many software packages have been designed to automate microarray data normalization and analysis. A commonly used program is Genespring (http://www. silicongenetics.com) which provides a fairly automated analysis process and allows the user to view and manipulate many microarray experiments at once. Another attractive benefit is that Genespring has the ability to produce many user-friendly graphical representations of the data. However, this software is costly, whereas there are many open-source alternatives freely available, such as the TM4 suite [45] from The Institute of Genomic Research (TIGR, www.tigr.org/software). TM4 contains four applications: TIGR Spotfinder, Microarray Data Analysis System (MIDAS), Microarray Data Manager (MADAM), and Multiexperiment Viewer (MeV). Also included is a Minimal Information About a Microarray Experiment (MIAME, see Section 2.5.8)-compliant database. These tools cover all aspects of image analysis through to data storage and we recommend them as a good alternative to commercially available software.

Alternatively, there are many programs or routines that have been designed by researchers and statisticians that act as pure statistical tools to crunch the raw data from a microarray experiment. These tools, unlike Genespring, put all aspects ofanalysis into the researchers hands, allowing a far more flexible analysis that is tailored to the experiment. Examples of these programs and routines include SMA (Statistics for Microarray Analysis, http://www.stat.berkeley.edu/ users/terry/zarray/Software/smacode.html), Bioconductor (http://www.biocon-ductor.org/), LIMMA (Linear Models for Microarray Data, http://bioinf.wehi. edu.au/limma/), and YASMA (Yet Another Statistical Microarray Analysis tool, http://people.cryst.bbk.ac.uk/wernisch/yasma.html). These are add-on packages that work in the "R" statistical environment (http://www.r-project.org/), so, although they are useful for data analysis, knowledge of the R language is required in order to exploit these tools fully.

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