Thanks, Gordon and Naomi. One of the examples in limma manual talks about 2x2 factorial experiments of a two-channel array. It estimates the interaction in the makeContrasts. > cont.matrix <- makeContrasts( + WT11.MT11=P11mt-P11wt, + WT21.MT21=P21mt-P21wt, + WT11.WT21=P21wt-P11wt, + MT11.MT21=P21mt-P11mt, + Int=(P21mt-P11mt)-(P21wt-P11wt), + levels=design) Since I got more factors (2x2x2x2), can I make the interactions with more factors (i.e. two-way, three-way, and four-way interactions)? Wei On Fri, Jan 16, 2009 at 11:10 PM, Naomi Altman <naomi@stat.psu.edu> wrote: > I think that Wei Xu is referring to the fact that one ANOVA is not an > identifiable model without a constraint - hence one either has to construct > the model matrix with an indicator variable, or with the factor effects. > > In limma, this does not matter, because limma does the overall F-test and > then allows you to construct as many contrasts as are reasonable. > > I always use single channel analysis for loop designs, which makes it > easier to set up the main effects and interactions. > > This was a kind of "statsy" comment on my part, but I hope that those who > have taken a course including factorial designs can follow. > > --Naomi > > > > At 10:33 PM 1/16/2009, Gordon K Smyth wrote: > > Date: Thu, 15 Jan 2009 16:12:08 -0500 >>> From: Wei Xu <xuwei3@msu.edu> >>> Subject: [BioC] reference argument in limma factorial design >>> To: bioconductor@stat.math.ethz.ch >>> Content-Type: text/plain >>> >>> Hi, everyone, >>> >>> I am working on a dual-channel cDNA microarray project which includes 32 >>> slides as a loop design. It is a 2x2x2x2 factorial experimental design >>> that >>> combines 16 treatments. When I was trying to use modelMatrix to design >>> the >>> matrix, it always asked me to input a reference. However, in my >>> experiment, >>> I don't really have one as a reference. I tried to assign a random >>> treatment >>> as reference but that way I couldn't make contrasts of the reference with >>> the other treatments. >>> >> >> Yes, you can make contrasts between the reference and other treatments, in >> fact that is what the coefficients now mean. Please refer to the examples >> on common reference designs in the limma User's Guide (for example Section >> 7.3), or past advice given on this list. >> >> Best wisehs >> Gordon >> >> How should I set this argument? Is there a different >>> way that allows me not to assign a reference? Thanks. >>> >>> Wei >>> >>> -- >>> Wei Xu >>> Aquatic Animal Health Laboratory >>> Pathobiology and Diagnostic Investigation >>> College of Veterinary Medicine >>> Michigan State University >>> East Lansing, MI, 48824 >>> Tel: 1-517-432-8258 >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111 > > > -- Wei Xu Aquatic Animal Health Laboratory Pathobiology and Diagnostic Investigation College of Veterinary Medicine Michigan State University East Lansing, MI, 48824 Tel: 1-517-432-8258 [[alternative HTML version deleted]]