[BioC] timecourse pkg question

[aaron.j.mackey at gsk.com]

I'm using the timecourse library to calculate Hotelling's T2 statistics, 
and would like to convert these to P values (and, ultimately, perform 
FDR).

For a 4 time point, 3 replicates (control and treated each), 54K gene 
experiment, I'm struggling with the appropriate variables for 
transformation.

This paper:

  http://bioinformatics.oxfordjournals.org/cgi/content/full/21/14/3105

provides an equation (see below) in J (# of genes), and number of 
replicates in treated (nD) and control (nN), but (incorrectly) leads to 
negative F values.

Thanks to anyone else who has already solved this,

-Aaron

P.S. Relevant extract from the above paper: (apologies if this doesn't 
come through well):