[BioC] F values from topTable with coef=NULL testing all zero or all equal?

James W. MacDonald jmacdon at med.umich.edu
Tue Oct 25 15:11:36 CEST 2011

Hi Michael,

On 10/24/2011 3:21 PM, Michael Muratet wrote:
> Greetings
> This has probably been answered before, but I can't narrow the search 
> down enough to find it in the archives. I am looking at the output 
> from and documentation for eBayes and realized that the null 
> hypothesis for the F statistic is that all the expression values are 
> zero. I want to test the hypothesis that all the expression values are 
> equal, i.e., rejection implies differential expression. I see from the 
> topTable documentation that calling it with coef=NULL will yield an F 
> statistic calculation, and I infer from the docs it will include all 
> the conditions. What is the null hypothesis: that all the values are 
> equal, or that all the values are zero?

I think you misunderstood the help for eBayes(). It states that the 
F-statistic tests that all _contrasts_ are zero, which is not the same 
as all expression values equal to zero (which wouldn't make sense).

If a contrast is equal to zero, it implies no differential expression 
between the samples compared in that contrast (or more correctly, a 
sufficiently small F-statistic implies that you are unable to reject the 
null hypothesis of a difference in any contrast). Note that you are only 
testing those contrasts that you specified via a contrasts matrix, or 
specified indirectly via your design matrix.



> Thanks
> Mike
> Michael Muratet, Ph.D.
> Senior Scientist
> HudsonAlpha Institute for Biotechnology
> mmuratet at hudsonalpha.org
> (256) 327-0473 (p)
> (256) 327-0966 (f)
> Room 4005
> 601 Genome Way
> Huntsville, Alabama 35806
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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