[BioC] F values from topTable with coef=NULL testing all zero or all equal?
Michael Muratet
mmuratet at hudsonalpha.org
Tue Oct 25 17:57:13 CEST 2011
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
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