[R] limma - OneWayAnova

James W. MacDonald jmacdon at med.umich.edu
Fri Apr 28 18:04:30 CEST 2006

Hi Max,

Max Kauer wrote:
> I have a very basic question about limma.
>     Assume I have experiments from 3 or more RNA sources in a reference
> design. It is easy to define individual contrasts but I want to specify a
> contrast matrix that tests for significant differences among ALL the
> different RNA sources (i.e. the analogous thing to a simple One-Way ANOVA).
> How can I do that?
> Thanks!
> Max

Although limma is available on CRAN, it is primarily a Bioconductor 
package, so this question is better asked on the BioC listserv.

As for your question, a simple one-way ANOVA doesn't test for 
significant differences between all factor levels - it tests for _any_ 
difference between factor levels. The only way to test for significant 
differences among all the factor levels is to construct a contrasts 
matrix that includes all possible comparisons. You could then use 
decideTests() with method = "nestedF" and look for those genes that are 
significant in all contrasts.



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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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