Dear BioC, I want to perform a Significance Analysis for Microarray, SAM, and I wonder which package to use. I read the vignette from "siggenes" package, but there is no way to implement fold change, FC, in the analysis as defaut. I subindexed the eset, according to fold change, of gens, but of course in this way I will affect the results of the permutation test. Is this the correct way to perform SAM, or I shold move to "samr"? is it package able to handle FC analysis in a different way? Thank you -- Claudio Isella ___________________________________________________________________ Salva ora il tuo preventivo gratuito Direct Line e assicurati lo sconto extra 5+5% sulla polizza auto! http://click.libero.it/directline2

Hi Claudio, by default, the fold change is computed in sam (it is called R.fold in the output). However, the fold change can also be used as a filtering criterion (similar to what Tusher et al. do) by specifying R.fold in sam by another value than 1. For details, see the argument R.fold in the help of sam.dstat. Best, Holger -------- Original-Nachricht -------- Datum: Tue, 29 Aug 2006 14:56:01 +0200 Von: "claudio\\.is\\@libero\\.it" <claudio.is at="" libero.it=""> An: "bioconductor" <bioconductor at="" stat.math.ethz.ch=""> Betreff: [BioC] SAM: siggenes and samr > Dear BioC, > > I want to perform a Significance Analysis for Microarray, SAM, and I > wonder which package to use. I read the vignette from "siggenes" package, but > there is no way to implement fold change, FC, in the analysis as defaut. I > subindexed the eset, according to fold change, of gens, but of course in > this way I will affect the results of the permutation test. Is this the > correct way to perform SAM, or I shold move to "samr"? is it package able to > handle FC analysis in a different way? > > > Thank you > > -- > Claudio Isella > > > ___________________________________________________________________ > Salva ora il tuo preventivo gratuito Direct Line e assicurati lo sconto > extra 5+5% sulla polizza auto! > http://click.libero.it/directline2 > > _______________________________________________ > 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 -- Echte DSL-Flatrate dauerhaft f?r 0,- Euro*. Nur noch kurze Zeit!