Significance Analysis of Microarrays (SAM) using Matlab

SAM is a popular method of finding differentially expressed genes through a microarray experiment.

In BioInformatics, one of the goal of a microarray experiment can be of finding those genes which are up-regulated or/and down-regulated. SAM is a method suggested by Tusher et al.(2001) achieving that goal, and has two implementation in the R programming language. Since SAM is not yet implemented in Matlab, we provide its first implementation based on the BioConductor project library siggenes, thanks to Holger Schwender (2012) for his permission.

To see extended explanation of the proposed implementation, please see the demo file "SAM_demo.m".

References.

Virginia Goss Tusher, Robert Tibshirani, Gilbert Chu (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences 98(9): 5116-5121.

Holger SCHWENDER (2012). siggenes : Multiple testing using SAM and Efron's empirical Bayes approaches. R package version 1.32.0.