Hi EdgeR community: I'm reading the edgeR manual<http: www.bioconductor.org="" packages="" release="" bioc="" vignettes="" edg="" er="" inst="" doc="" edgerusersguide.pdf=""> and have a question: In example page 31: "3.5 Comparisons Both Between and Within Subjects" After estimating the dispersions (*code not shown*), we can fit a linear model: .... Should the "*code not shown" *in this case be: > y <- estimateGLMCommonDisp(y,design) > y <- estimateGLMTrendedDisp(y,design) > y <- estimateGLMTagwiseDisp(y,design) Thank you! Son. [[alternative HTML version deleted]]

Hi Son, That's the old way of doing things. These days you can just do y <- estimateDisp(y, design) And I think the code is not shown there because it has been shown many times prior to that point in the document, and doesn't really change unless you have some reason to change from the default arguments. Best, Jim On Thursday, March 06, 2014 6:16:24 AM, Son Pham wrote: > Hi EdgeR community: > I'm reading the edgeR > manual<http: www.bioconductor.org="" packages="" release="" bioc="" vignettes="" e="" dger="" inst="" doc="" edgerusersguide.pdf=""> > and > have a question: > In example page 31: > "3.5 Comparisons Both Between and Within Subjects" > After estimating the dispersions (*code not shown*), we can fit a linear > model: .... > > Should the "*code not shown" *in this case be: > >> y <- estimateGLMCommonDisp(y,design) >> y <- estimateGLMTrendedDisp(y,design) >> y <- estimateGLMTagwiseDisp(y,design) > Thank you! > Son. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099