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

[Michael Muratet]

On Oct 25, 2011, at 8:11 AM, James W. MacDonald wrote:

> 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.
>
> Best,
>
> Jim
Thanks, I understand it now.
M
>
>
>>
>> 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.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
>
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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