





Hi Gordon,
If I have multiplex time points, when set coeff to "NULL" in topTable function, it return results (named as R1) from F-statistics, however, if I set coeff to each time point, one by one, then I get DEG in each time point (named as R2, combined all DEG symbol in one list). Then, R1 and R2 have some overlap, but R2 usually has more genes that excluded in R1. ?So, in this case, which approach back correct DEG gene list? ?

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
?发件人：?Joseph J Hou发送时间：?2014-02-17?10:30收件人：?smyth抄送：?bioconductor主题：?limma for time course dataset
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


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