SAM: Significance Analysis of Microarrays

• SAM manual
  
  
• Developed at Stanford University Labs: based on recent paper of Tusher, Tibshirani and Chu (2001):
  "Significance analysis of microarrays applied to the ionizing radiation response" (ps file). (pdf version). PNAS 2001 98: 5116-5121, (Apr 24). "Raw data"
  
  
• Correlates gene expression data to a wide variety of clinical parameters including
  treatment, diagnosis categories, survival time and time trends
  
  
• Provides estimate of False Discovery Rate for multiple testing
  
  
• Convenient Excel Add-in
  
  
• Works with data from both cDNA and oligo microarrays. Can also be applied to protein expression data and SNP chip data.
  
  
• Patent Pending for SAM technology
  
  
• SAM uses the FDR and q-value method presented in Storey (2002) A direct approach to false discovery rates. J. Roy. Stat. Soc. Ser. B, 64:479-498;
  
  Local false discovery rates proposed in Efron, B., Tibshirani, R., Storey, JD, and Tusher, V. (2001). Empirical Bayes Analysis of a Microarray Experiment, JASA, 96, 1151-1160 and Efron and Tibshirani, Microarrays, Empirical Bayes Methods, and False Discovery Rates" Genet. Epidemiol. 2002 Jun;23(1):70-86;
  
  and Miss rates--- Jon Taylor, Rob Tibshirani and Brad Efron. The ``Miss rate'' for the analysis of gene expression data; Biostatistics 2005 6(1):111-117.

 

• List of features

   

• R package samr

   

• Sample screens

   

• Frequently Asked Questions

   

• ``Samster'' tool

   

• Euan Ashley's heatmap builder

   

• Related links: PAM package for microarray classification;
  CGH-Miner package for CGH data;
  PPC package for protein mass spec classification
  Superpc package for microarray prediction;

Obtaining SAM

• Academic users can download SAM by going directly to the registration page. Please note that this is the full version!
• Non academic users should first register via the registration page. An evaluation version (limited to 500 genes) can be downloaded directly from that page.

  If you are a commercial user and wish to obtain a complete version of SAM, proceed to the SAM resource at the Office of Technology and Licensing. The SAM contact is Sara Nakashima (sara.nakashima@stanford.edu) at the Office of Technology and Licensing, Phone: (650) 725-9117.

  Please do not contact Sara Nakashima about downloading, technical questions etc. All she handles is commercial licensing!

• Returning users (those who have already registered) who want to download the software again can proceed directly to the Academic Download Page or the Non-Academic Download Page. You will need the registration information that you received via email.