[BioC] Very low P-values in limma

[Gordon K Smyth]

On Sat, 24 Oct 2009, Gordon K Smyth wrote:

> Dear Paul,
>
> Give your consensus correlation value, limma is treating your within-array 
> replicates as worth about 1/3 as much as replicates on independent arrays 
> (because 1-0.81^2 is about 1/3).

Sorry, my maths is wrong.  The effective weight of the within-array 
replicates is quite a bit less than 1/3, given ndups=4 and cor=0.81.

Best wishes
Gordon