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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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor --