Significance Analysis of Dose-Response Microarray Data

The significance analysis of microarrays (SAM) Tusher et al. (Proc Natl Acad Sci 98:5116–5121, 2001) is a widely used testing procedure that estimates the FDR by using permutations under the assumption that all null hypotheses are true. The procedure consists of three components: (1) the adjusted test statistics, (2) an approximation of the distribution of the test statistics based on permutations, and (3) the control of the FDR. In Chap. 8, we discuss the implementation SAM for the setting of dose-response microarray experiments and illustrate how to use the IsoGene package for SAM.