Hi Assa, For myself, I find formulating the design matrix like this to be very accessible: # define the factors with names (extended from James version) condition <- factor(rep(c("wt","LiCl"), each = 3, times = 3)) group <- factor(rep(c("total","low","high"), each = 6)) # concatenate factor combinations together combinations <- paste(condition, group, sep=".") # create factors from combinations f <- factor(combinations, levels=unique(combinations)) design <- model.matrix(~0+f) # beautify column names colnames(design) <- levels(f) design wt.total LiCl.total wt.low LiCl.low wt.high LiCl.high 1 1 0 0 0 0 0 2 1 0 0 0 0 0 3 1 0 0 0 0 0 4 0 1 0 0 0 0 5 0 1 0 0 0 0 6 0 1 0 0 0 0 7 0 0 1 0 0 0 8 0 0 1 0 0 0 9 0 0 1 0 0 0 10 0 0 0 1 0 0 11 0 0 0 1 0 0 12 0 0 0 1 0 0 13 0 0 0 0 1 0 14 0 0 0 0 1 0 15 0 0 0 0 1 0 16 0 0 0 0 0 1 17 0 0 0 0 0 1 18 0 0 0 0 0 1 This gives you a matrix where every factor combination has a separate column. After you create the fit you can easily create your contrasts of interest using the column names, e.g. for the comparison of the total: cont.matrix <- makeContrasts(WTvsLiClTotal=wt.total-LiCl.total, levels=design) fit2 <- contrasts.fit(fit, cont.matrix) For your case I would suggest reading the excellent Limma userguide: "Chapter 8.7 Factorial Designs" which explains the the different design matrices and upon which my example is based on. Hope that helps. Cheers, Walter On 03.01.2012 16:47, Assa Yeroslaviz wrote: > Hi James, > > Thanks for the answer. > I like the first idea of having the design matrix more flexible. The > problem I have with understanding it, regards the different columns. > How can I compare two conditions using this matrix. > If I understand it correctly, I have the wt in the first column and the and > the LiCl in the second one. The third column contains the 'low' and the > fourth the 'high' files. > > First question - what about the 'total' files - how can I get to them with > this matrix? > > Second question - how can I for example can compare the wt.total with the > LiCl.total files (or the other two groups)? > > Thanks > > Assa > > On Tue, Jan 3, 2012 at 16:08, MacDonald, James<jmacdon at="" med.umich.edu="">wrote: > >> Hi Assa, >> >> >> On 1/3/12 7:32 AM, Assa Yeroslaviz wrote: >> >>> Hi bioC User, >>> >>> I have a set of 18 Affymetrix arrays with three different conditions. The >>> annotation looks like that: >>> number condition group >>> 19 wt total >>> 20 wt total >>> 21 wt total >>> 22 LiCl total >>> 23 LiCl total >>> 24 LiCl total >>> 25 wt low >>> 26 wt low >>> 27 wt low >>> 28 LiCl low >>> 29 LiCl low >>> 30 LiCl low >>> 31 wt high >>> 32 wt high >>> 33 wt high >>> 34 LiCl high >>> 35 LiCl high >>> 36 LiCl high >>> >>> for each of the groups total, low and high I would like to compare wt vs. >>> LiCl (treatment). >>> I was trying to create a design matrix for the complete data set, but >>> somehow I am mixing everything up. >>> >>> Can someone please help me with the with the correct construction of the >>> design matrix. >>> >>> >> The easiest way is to use the model.matrix() function. >> >> What I would normally do is this: >> >> condition<- factor(rep(1:2, each = 3, times = 3)) >> group<- factor(rep(1:3, each = 6)) >> >> design<- model.matrix(~ 0 + condition + group) >> >> Because that will allow more comparisons than what you want. However, it >> is easy enough to get what you want: >> >> >> design<- model.matrix(~0 + factor(rep(1:6, each = 3))) >> >> colnames(design)<- paste(rep(c("wt","LiCl"), 3), >> rep(c("total","low","high"), each = 2), sep = ".") >> >> You will note that the design matrix you get is not the same as what you >> have below, because you cannot have a column of zeros. >> >> Best, >> >> Jim >> >> >> >> If I understand it correctly it should looks like this: >>> 1 0 0 0 0 0 0 >>> 1 0 0 0 0 0 0 >>> 1 0 0 0 0 0 0 >>> 0 1 0 0 0 0 0 >>> 0 1 0 0 0 0 0 >>> 0 1 0 0 0 0 0 >>> 0 0 1 0 0 0 0 >>> 0 0 1 0 0 0 0 >>> 0 0 1 0 0 0 0 >>> 0 0 0 1 0 0 0 >>> 0 0 0 1 0 0 0 >>> 0 0 0 1 0 0 0 >>> 0 0 0 0 1 0 0 >>> 0 0 0 0 1 0 0 >>> 0 0 0 0 1 0 0 >>> 0 0 0 0 0 1 0 >>> 0 0 0 0 0 1 0 >>> 0 0 0 0 0 1 0 >>> >>> But somehow I can neither create it nor write the right header. >>> I would appreciate your help >>> >>> Thanks >>> Assa >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> >> ************************************************************ >> Electronic Mail is not secure, may not be read every day, and should not >> be used for urgent or sensitive issues >> > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > -- ------------------------------------------------------------- Dr. Walter Glaser Max F. Perutz Laboratories Department of Medical Biochemistry Medical University of Vienna Dr. Bohrg. 9/2 1030 Vienna AUSTRIA