Hi, I don't believe that you can meaningfully test main effects using a model that includes an interaction term (as yours does). If I recall correctly, in order to test main effects, you would have to fit an additive model such as "~Diet + Disease", and any results from that model will not be valid for genes with a significant interaction. -Ryan On Fri 11 Jul 2014 09:12:27 AM PDT, kaushal Chaudhary [guest] wrote: > 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor