Dear all,

I am wondering what is the difference between the SAM used in the package
siggenes and the SAM used in sam2.20. I raised this concern since I read a
relative new paper: A comprehensive evaluation of SAM, the SAM R-package and
a simple modification to improve its performance. The paper mentioned about
the poor estimation of FDR of SAM (the method in the original paper), while
also pointing out that the sam2.20 from the Stanford website is actually
using different FDR estimation than the one mentioned in the original SAM
paper. I have been using the "SAM" in the siggenes package for awhile, just
wondering if this is similar to sam2.20, and if it is still reasonable for
me to continue using it....... any further thoughts or suggestions about all
the SAM softwares available ?

Thanks a lot,
Alex -




-- 
Lam C. Tsoi (Alex)
Medical University of South Carolina

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