Differential expression

• The CyberT program in Baldi and Long (20) with a web interface can be downloaded from visitor.ics.uci.edu/genex/cybert/. It is also available as R code hdarray.

• The MB-statistic and T2 statistic (34) will be implemented in the Bio-conductor package timecourse www.stat.berkeley.edu/users/terry/Group/ research/timecourse.html.

• The B-statistic (24, 29) and moderated F-statistic (29) are implemented in the Bioconductor package limma. The latest limma can be downloaded from bioinf.wehi.edu.au/limma/. LimmaGUI and affylmGUI (81) are two nice graphical user interfaces to limma for two-color arrays and Affymetrix chips, respectively.

• The empirical Bayes method across multiple independent groups in Kendziorski et al. (27) is available through the Bioconductor package EBarrays.

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