[BioC] reference argument in limma factorial design

Naomi Altman naomi at stat.psu.edu
Sat Jan 17 05:10:48 CET 2009

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.


At 10:33 PM 1/16/2009, Gordon K Smyth wrote:

>>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 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 at stat.math.ethz.ch
>Search the archives: 

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
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