Hi,
  I am using the package samr for multiclass problem. My dataset is the srbct data with 63 samples distributed in 4 classes, there are 2308 genes. I have the following questions:
1. It seems that there are only up-regulated genes, why is this?.
2. In the variable siggenes.table$genes.up, there are some column names like "contrast-1", "contrast-2", "contrast-3", "contrast-4". What do they mean? 
3. Is the fudge factor s0 calculated the same way as two class problem? I coded my own R code and have excellent agreement with what the samr package calculates for two class problem for the calculation of s0, I apply the same strategy to the multiclass problem, but I can not seem to get the same results as the samr package. 
4. How exactly SAM is calculated in multiclass problem? Is that just adding a fudge factor to the F-like statistics? 

Many thanks,
James

 
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