[BioC] conditions to apply BH correction

[Loredana Le Pera]

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.