MatSAM: a Matlab implementation for Significance Analysis of Microarrays

Eric Nimpaye, Ouafae Kaissi, Tiratha Raj Singh, Brigitte Vannier, Azeddine Ibrahimi, Ahmed Moussa

Abstract


Microarray experiments enable the simultaneous measure of expression levels of large amount of genes and have many applications. A widespread one is finding set of genes that are differentially expressed. Significance Analysis of Microarrays (SAM) helps to produce those sets using multiple testing techniques. There is unfortunately not yet a public tool enabling to do SAM using the Matlab platform. We here define MatSAM, a SAM implementation in Matlab, and show that it yields results of high confidence comparatively to those obtained by putative tools available in the R programming environment. MatSAM can be used in conjunction with Matlab Bioinformatics toolbox to perform further analysis.

Availability: MatSAM is available as source code at  http://www.bioinfoindia.org/MatSAM

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