[BioC] SAM vs. sam2.20

Holger Schwender holger.schw at gmx.de
Fri Sep 14 13:24:12 CEST 2007


Hi Alex,

I know neither the article you have mentioned nor sam2.20. I only can speak for SAM as implemented in siggenes. A brief description of the SAM algorithm as implemented in siggenes is available in Section 6.3.2 of my PhD thesis

http://hdl.handle.net/2003/23306 

Please read this description and decide yourself if you would like to use SAM as implemented in siggenes again.

Best,
Holger


-------- Original-Nachricht --------
> Datum: Thu, 13 Sep 2007 16:43:25 -0400
> Von: "Alex Tsoi" <tsoi.teen at gmail.com>
> An: bioconductor at stat.math.ethz.ch
> Betreff: [BioC] SAM vs. sam2.20

> 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
> 
> 	[[alternative HTML version deleted]]
> 
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