Running SAM
- SAM is available for download online at http://www-stat.stanford.edu/~tibs/SAM/ for academic and non-academic users after completion of a registration step.
- SAM is run as an Excel Add-In, and the SAM Plot Controller allows Customization of the False Discovery Rate and Delta, while the SAM Plot and SAM Output functionality generate a List of Significant Genes, Delta Table, and Assessment of Sample Sizes
- Permutations are calculated based on the number of samples
- Block Permutations
- Blocks are batches of microarrays; for example for eight samples split into two groups (control and affected) there are 4!=24 permutations for each block and the total number of permutations is (24)(24)= 576. A minimum of 1000 permutations are recommended;
the number of permutations is set by the user when imputing correct values for the data set to run SAM
Read more about this topic: Significance Analysis Of Microarrays
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