Dear Bioconductors Friends! I did a parametrization, based on 8.7 Factorial Designs section on limma usersguide, in a 2x2x2x4 factorial experiment and I would like to ask you if I did a correct script for limma. Here is my targets file: http://www.divshare.com/download/3986449-8af And here is my script file: http://www.divshare.com/download/3986693-8ea My doubts are on how to I could interpret the topTable out put based on my contrasts! --- topTable(fit2,coef=1,number=10) coef=1 = Sus.H2O.Inoc.0-Sus.H2O.Ctrl.0 Here are the genes which respond to Inoc on Time 0, Sus, and H20. There aren't interactions here. True? The genes up- or down-regulated in topTable are up or down-regulated in "Sus.H2O.Inoc.0" or in "Sus.H2O.Ctrl.0"? --- topTable(fit2,coef=17,number=10) coef=17 = (Sus.BION.Inoc.0-Sus.BION.Ctrl.0)-(Sus.H2O.Inoc.0-Sus.H2O.Ctrl.0) Here are the genes which respond to BION and Inoc on Sus and Time 0, or here are the interaction between BION and Inoc (Var:Ind) on Sus and Time 0. True? The genes up- or down-regulated in topTable are up or down-regulated in "(Sus.BION.Inoc.0-Sus.BION.Ctrl.0)" or in "(Sus.H2O.Inoc.0-Sus.H2O.Ctrl.0)"? --- topTable(fit2,coef=25,number=10) coef=25 = ((Res.BION.Inoc.0-Res.BION.Ctrl.0)-(Res.H2O.Inoc.0-Res.H2O.C trl.0))-((Sus.BION.Inoc.0-Sus.BION.Ctrl.0)-(Sus.H2O.Inoc.0-Sus.H2O.Ctr l.0)), Here are the genes which respond to Res and BION and Inoc on Time 0, or here are the interaction between Res and BION and Inoc (Var:Ind:Trat) on Time 0. True? The genes up- or down-regulated in topTable are up or down-regulated in "((Res.BION.Inoc.0-Res.BION.Ctrl.0)-(Res.H2O.Inoc.0-Res.H2O.Ctrl.0))" or in "((Sus.BION.Inoc.0-Sus.BION.Ctrl.0)-(Sus.H2O.Inoc.0-Sus.H2O.Ctrl.0))"? Could I extract all interactions? May be that this are basics questions, but I am very insecure with they. Could you suggest anything here? Thank you so much! -- Marcelo Luiz de Laia Jaboticabal - SP - Brazil sip:marcelolaia at ekiga.net "Voc? v? as coisas como elas s?o e pergunta: por qu?? Mas eu sonho com coisas que nunca foram e pergunto: por que n?o? " - Bernard Shaw