Hi?Gordon, My project is time course dataset, 9 time points and 21 subjects. When I use "topTable" function to call differential genes, how to set argument "coeff" ? If I set it as each time point (column name specifying) one by one, it'll reture results by t-test. ??If I set to as "NULL", topTable will use F-ststistic to rank genes with all coefficient, and usually the difference gene by F- test will smaller than t-test by each time points. I'm worry about F-ststistic will miss some of meaning informations. So, as you suggestion, how to set the coeff parameter to time-course dataset, to find allover DEG and DEG in individual time point??p.s. Usually, in heatmap figure, log-Fold change or normalized intensity of each group used in visualization?? Best,Joe Joseph J Hou ---------------------------------------------- Jue Hou Ph.D. Research Assistant Center of Medical Physics and Technology Hefei Institutes of Physical Science Chinese Academy of Sciences No.350 Shushanhu Road,Shushan District,Heifei,P.R. China Tel. +86551-65595385 Email: joseph.houjue@gmail.com; houjue@cmpt.ac.cn [[alternative HTML version deleted]]