Hello, In my micro array expriemt, I have four different types of samples (nodiet.nodisease, nodiet.disease, diet.nodisease, and diet.disease). I want to make the following 5 comparisons. Diet.nodisease vs. nodiet.nodisease (effect of diet in no disease) Diet.disease vs. nodiet.disease (effect of diet in disease) Nodiet.disease vs. Nodiet.nodiease (effect of disease in no diet) Diet.disease vs. Diet.nodisease (effect of disease in diet) Diet.disease vs. nodiet.nodisease I used makecontrasts function in limma in R. Contrast.matrix=makecontrasts( Diet.nodisease vs. nodiet.nodisease= Diet.nodisease - nodiet.nodisease Diet.disease vs. nodiet.disease = Diet.disease - nodiet.disease Nodiet.disease vs. Nodiet.nodiease= Nodiet.disease -Nodiet.nodiease Diet.disease vs. Diet.nodisease= Diet.disease - Diet.nodisease Diet.disease vs. nodiet.nodisease= Diet.disease - nodiet.nodisease ) I also want to get the main effect of diet and disease and interaction at the same time. (diet, disease, diet*disease). I suppose the code gives 2 diet effects and 2 diseases effect. I would appreciate any advice. Thanks !!! -- output of sessionInfo(): None. -- Sent via the guest posting facility at bioconductor.org.

Dear Kaushal Chaudhary, The interaction is the contrast: IA = (diet.nodisease-nodiet.nodisease) - (diet.disease- nodiet.disease) I don't think that the main effects have any meaningful interpretation in your experiment. However they are defined by: Diet = (diet.nodisease-nodiet.nodisease+diet.disease- nodiet.disease)/2 Disease = (nodiet.disease-nodiet.nodisease+diet.disease- diet.nodisease)/2 It's pretty intuitive really. You simply add all the treatment conditions in which the factor is positive and subtract all the conditions in which the factor is negative. In other words, the main effect for Diet is just the average of the Diet effects in the disease and nodisease states respectively. Best wishes Gordon > Date: Fri, 11 Jul 2014 09:12:27 -0700 (PDT) > From: "kaushal Chaudhary [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, kaushal2040 at gmail.com > Subject: [BioC] Contrast matrix in limma > > Hello, > > In my micro array expriemt, I have four different types of samples (nodiet.nodisease, nodiet.disease, diet.nodisease, and diet.disease). I want to make the following 5 comparisons. > Diet.nodisease vs. nodiet.nodisease (effect of diet in no disease) > Diet.disease vs. nodiet.disease (effect of diet in disease) > Nodiet.disease vs. Nodiet.nodiease (effect of disease in no diet) > Diet.disease vs. Diet.nodisease (effect of disease in diet) > Diet.disease vs. nodiet.nodisease > I used makecontrasts function in limma in R. > Contrast.matrix=makecontrasts( > Diet.nodisease vs. nodiet.nodisease= Diet.nodisease - nodiet.nodisease > Diet.disease vs. nodiet.disease = Diet.disease - nodiet.disease > Nodiet.disease vs. Nodiet.nodiease= Nodiet.disease -Nodiet.nodiease > Diet.disease vs. Diet.nodisease= Diet.disease - Diet.nodisease > Diet.disease vs. nodiet.nodisease= Diet.disease - nodiet.nodisease > ) > > I also want to get the main effect of diet and disease and interaction > at the same time. (diet, disease, diet*disease). I suppose the code > gives 2 diet effects and 2 diseases effect. I would appreciate any > advice. > > Thanks !!! ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}