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

[Michael Muratet]

Begin forwarded message:

> From: Michael Muratet <mmuratet at hudsonalpha.org>
> Date: October 24, 2011 2:21:22 PM CDT
> To: bioconductor at r-project.org
> Subject: F values from topTable with coef=NULL testing all zero or  
> all equal?
>
> 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?
>
Hello again

I just realized that the test is on log differential expression, and  
rejecting the null hypothesis values equal to zero implies  
differential expression.

Cheers

Mike
> 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
>
>
>
>
>

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