Dear Gordon, I am very interested in "Comparisons Both Between and Within Subjects" of edgeR. Because one of my study is according to this design. But i found some detailed analysis have not been provided in the manual (After estimating the dispersions (code not shown), we can fit a linear model:), and i met some difficulty in using this pipline. When i use y <- estimateGLMCommonDisp(y, design, verbose=TRUE) to get the dispersion, i get an error. I wonder whether you can provide some detailed analysis process (especially in data reading, dispersion evaluation ). Thanks for your kind assistance. -------------- Huajing Teng Beijing Institutes of Life Science, Chinese Academy of Sciences Beichen West Road,Chao Yang District,Beijing 100101, China E-mail:tenghj at mail.biols.ac.cn 2013-01-04