[BioC] decideTests with nestedF

[Pedro López Romero]

Hi Sean, 

thanks a lot for the replay. 

Yes, you understood my doubt. I have several experimental conditions, and I
thought that filtering first by the moderated F-statistic would be a right
approach, since by this I would be selecting the genes that are DE in any of
the contrasts. Now, from this reduced list, I thought that I could select
the genes for every independent contrast given by my experimental
conditions. 

Now, I do not understand why this is not a valid strategy. In fact, I
understood that what limma user guide propose in p 51 (chapter 10) is doing
this but using decideTests ( ) with nestedF.-

Pedro.  



-----Mensaje original-----
De: Sean Davis [mailto:sdavis2 at mail.nih.gov] 
Enviado el: viernes, 16 de junio de 2006 13:04
Para: Pedro L ó pez Romero; Bioconductor
Asunto: Re: [BioC] decideTests with nestedF




On 6/16/06 5:30 AM, "Pedro López Romero" <plopez at cnic.es> wrote:

> Dear list, 
> 
>  
> 
> I have an experiment with several contrasts associated to different
> experimental conditions for each gene, so I want to select genes in a
first
> step by their moderated-F statistic in order to reduce the number of genes
> for multiple contrasts across genes.

Hi, Pedro.

If I understand what you are trying to do, choosing genes using F-stats like
this for later statistical testing is not really valid.  If you want to
reduce the number of genes for subsequent testing, you should be using an
unsupervised approach (like looking for high-variance genes, as one
example).  Did I misunderstand the approach you are trying to take?

Sean