[BioC] reference argument in limma factorial design

Gordon K Smyth smyth at wehi.EDU.AU
Sat Jan 17 04:33:20 CET 2009

> Date: Thu, 15 Jan 2009 16:12:08 -0500
> From: Wei Xu <xuwei3 at msu.edu>
> Subject: [BioC] reference argument in limma factorial design
> To: bioconductor at 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

> 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

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