Significance Analysis of Microarrays (SAM)
The IsoGeneGUI also provides testing for the dose-response relationship under order restricted alternatives using the Significance Analysis of Microarrays procedure (SAM, Tusher et al., 2001). To perform this analysis there are two main steps:
1. Calculating the SAM regularized test statistic using permutation
First, the five SAM regularized test statistics need to be calculated.
Analysis > Significance Analysis of Microarrays > SAM permutation
Screenshot of the SAM permutation dialog box

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Screenshot of the list of significant genes based on SAM procedure
2. SAM analysis
After the SAM regularized test statistics are computed or loaded from a file, the user can now perform the SAM analysis.
Analysis > Significance Analysis of Microarrays > SAM analysis
Screenshot of the main dialog box for SAM analysis