> Date: Wed, 14 Mar 2007 10:19:32 -0800 (PST) > From: "Sergio Barberan" <barberan at="" biology.ucsc.edu=""> > Subject: [BioC] Limma time course with two-color microarrays > To: bioconductor at stat.math.ethz.ch > > Dear list, > > It might be a really easy problem but I can not figure out how to do it. > > I'm trying to analyze a set of hybs of a time course experiment, where I > used a loop design. I have six samples and no reference, I compare > (1-2,2-3,3-4,4-5,5-6,6-1); each with dye swaps so I have 12 slides. > > By selecting sample 1 as my reference in modelMatrix, I get the following > design matrix: > > 2 3 4 5 6 > 1 0 -1 1 0 0 > 2 0 0 -1 1 0 > 3 0 0 0 -1 1 > 4 1 0 0 0 -1 > 5 0 1 0 0 0 > 6 0 0 0 1 -1 > 7 0 1 -1 0 0 > 8 -1 0 0 0 1 > 9 1 0 0 0 0 > 10 0 0 1 -1 0 > 11 0 -1 0 0 0 > 12 -1 0 0 0 0 > > My question is: How to use contrastMatrix to obtain the following > comparisons: 1-2, 2-3, 3-4, 4-5, 5-6 and 6-1? You just have to remember that each column of your design matrix is already a contrast vs 1. So you need cont.matrix <- makeContrasts(-2,2-3,3-4,4-5,5-6,6,levels=design) HOWEVER, to make this work the column names of the your design matrix must start with a letter, not a number. E.g., you need "Time2", "Time3" etc instead of "2", "3" etc. > I know there is some information about Limma and time course experiments > but that example uses one-color arrays so I'm confused about how to apply > that to my experimental design. The two colour is the same as the one-colour from this point. Best wishes Gordon > Thanks in advance for any help, > Sergio