other choices include factDesign daMA which both are (as I understand it) more directed towared factorial designs Robert On Feb 8, 2005, at 2:38 AM, <arne.muller@sanofi-aventis.com> wrote: > Hello, > > look at the limm package and browse the lists archive for > postings/questions on limma. It's a linear model that adjusts variance > via other genes on the chip (I hope I got this right ...) and probably > performs better than "lm/anova". It's one of the most frequently used > packages for finding differentially expressed genes. It also works > single and two channel arrays. > > Arne > >> -----Original Message----- >> From: bioconductor-bounces@stat.math.ethz.ch >> [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of Jakub >> Orzechowski >> Sent: 08 February 2005 11:21 >> To: bioconductor@stat.math.ethz.ch >> Subject: [BioC] factorial analysis of affy arrays >> >> >> Hi! I'm doing some experiments with affy arrays, with a 2*2*2 >> factorial >> design. Which tools are available for analysis of such experiments? >> Which methods can you recomended? What about ANOVA stuff from >> YASMA? Any >> other suggestions? >> >> thanks >> Jakub Orzechowski >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+