Software for microarray data analysis (no date) [incomplete]

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R and the Bioconductor package

There is a wide range of software available for the analysis of microarrays. I will use Bioconductor which is a set of libraries for a statistical programming language called R. Both Bioconductor and R are open source, which means that you can obtain the pacakge at no cost. Open source also means that you can modify the program, if you are so inclined, to add new features. Most of us (myself especially) do not have the programming skills to modify Bioconductor or R, but there are scores of graduate students and faculty who do have this skill and who open source software as a way to quickly publicize and promote their research. As a result, R and Bioconductor have some of the best and most cutting edge analysis methods around.

Instructions for setting up R on your computer are on the web at

• http://www.r-project.org/

For Windows users, this simply means downloading and running an install program. To install Bioconductor, type in the following two commands:

• source("http://www.bioconductor.org/getBioC.R")
• getBioC()

This will get the default set of packages. You can install a particular set of packages, such as the "affy" packages by typing in

• getBioC(libName="affy")

and if you have a high speed connection and some free time,  you can download the entire Bioconductor system by typing

• getBioC(libName="all")