Statistical Analysis of Microarrays (SAM)

I’m trying to analyze microarray data from three treatment groups with SAM. I’ve having trouble with a few steps:

  1. I’m pretty sure that I need to use multiclass, but there is no option for telling SAM that the data are log2. Does this matter?

  2. Three columns of contrast numbers are given for the gene lists. The instructions for SAM say to compare these to the null values to determine which contrasts are significant. Does this mean that any contrast values outside of the 2.5 and 97.5% are significant?