Dear Paul
You shouild take into account that you are doing very noisy statistics in
first place (a common problem in highthrouput genomics), Did you apply
eBayes? from limma
Elmer

On Wed, Oct 21, 2009 at 3:36 PM, Paul Geeleher <paulgeeleher@gmail.com>wrote:

> Hi folks, I'm analyzing microRNA data using limma and I'm wondering about
> the validity of the p-values I'm getting out. Its a simple 'Group A Vs
> Group
> B' experimental design. 4 arrays in one group, 3 in the other and 4
> duplicate spots for each miRNA on each array.
>
> The lowest adjusted p-values in the differential expression analysis are in
> the region of 10^-7.
>
> Its been pointed out to me that plugging the point values from each sample
> into a regular t-test you get p=0.008, which then also needs to take the
> multiple test hit. Can anybody explain why limma is giving me such lower
> values and if they are valid?
>
> I can provide more information if required.
>
> Thanks,
>
> Paul.
>
> --
> Paul Geeleher
> School of Mathematics, Statistics and Applied Mathematics
> National University of Ireland
> Galway
> Ireland
>
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-- 
Elmer A. Fernández (Bioing. PhD)
Investigador Asistente CONICET - Research Assistant CONICET
Porf. Inteligencia Artificial -UCC - Prof. Artificial Intelligence @ UCC
tel: +54-(0)351-4938000 int 145
Fax: +54-(0)351-4938081
web page : http://www.uccor.edu.ar/modelo.php?param=3.8.5.15
mail address: Camino Alta Gracia Km 7.1/2- Córdoba-5000-Argentina

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