[BioC] decideTests with nestedF

[Sean Davis]

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