Hi Loredana ,

1. Positive dependence is also Ok.
2.  under the null hypothesis, the distribution of the p-values is
Uniform[0,1] - it can be proved.
So this is assumption of the method, you do not have to check it.

Pavel



On Thu, May 12, 2011 at 5:11 PM, Loredana Le Pera
<loredanalepera@gmail.com>wrote:

> Dear List,
>
> I would like to understand if/when Benjamini-Hochberg correction can be
> applied and if not, what kind of correction is possible to apply.
>
> From the oneChannelGUI package vignette:
>
> "The function raw p-value distribution is implemented to evaluate if the BH
> type I error correction methods could be used. To apply BH correction two
> conditions should be satisfied:
> 1. The gene expressions are independent from each other.
> 2. The raw distribution of p-values should be uniform in the non
> significant range."
>
>
> My doubts mainly concern the second condition:
>  - what does it mean exactly?
>  - where does it come from?
>
> If this condition is not true, what  I can do to consider multiple testing
> correction?
>
>
> Thanks for any reply or suggestion,
> Loredana.
>
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