What software can be used to analyze microarrays?
There are a number of packages out there to help analyze microarray data depending on your microarray platform, statistics expertise, and cost. • Bioconductor is a great open source package of different packages built on top of the R statistical programming language. Bioconductor’s contributors have done a really nice job of delivering cutting edge algorithms to people in a usable package. Being based on R, which is a command line interface, means that it takes a little learning to get up to speed, but they have a lot of really useful documentation including a short course on microarray analysis presented by Robert Gentleman, Wolfgang Huber, and Zhijin (Jean) Wu who are prominent in the microarray community. Some of the more populare packages include: • affy – Methods for Affymetrix oligonucleotide arrays including the ever popular RMA analysis method. • geneplotter – Grapics related functions for Bioconductor. • limma – Linear Models for microarray data, contains methods for doing dif
