Hi,
  I am a new user to SAM and have one question on how to calculate s0. I saw from the originial SAM paper that s0 is used to minimize the coefficient of variation of d. I tried to write R code to reproduce the results calculated by R package SAMR. The current status is that if I use fix s0 in both my own R code and SAMR package, I got identifical results for gene list. However, if I estimate s0 by the method mentioned in the paper to minimize the CV of d, I got different results than the using default setting in SAMR package. I saw from other places the calculation of s0: "choose s0 to make the cv of d(i) approximately constant" and get confused by this. My understanding is that for each s0, there is a corresponding d with length number of genes, and there is one value of coefficient of variation of d, changing s0 will get different d and CV(d). Which point should I choose in the curve of s0 vs. cv(d)? I chose the s0 which makes the minimum cv(d), but got different answer
 using my own R code from using the default setting in SAMR package. Could anybody explain to me EXACTLY how should I choose s0 and EXACTLY how the s0 in the default setting of SAMR calculated? I am pretty frustrated by this. 

  Many thanks,
  James

 
  
  
 		
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