[BioC] Two-way ANOVA with multtest's MTP/EBMTP

[Neil Gray]

Hello - hopefully a quick question here.  I've been using the MTP and 
EBMTP functions for multiple testing correction of microarray 
expression data.  I've had no problems using the t-test option, but  my 
overall design is a two-factor ANOVA (2x2 groups using two  different 
treatments).  My eSet therefore has two phenoData slots, and while it's 
easy enough to specify one or the other, e.g., 
test='t.twosamp.equalvar' and Y='treatment1', but I don't understand how 
to specify the 2x2 design for  test='f.twoway'.   It seems Y can't be a 
matrix, and it can only be of  length equal to the number of samples.

So, given that 12 samples with groups defined as 
treatment1=c(0,0,0,0,0,0,1,1,1,1,1,1) and 
treatment2=c(0,0,0,1,1,1,0,0,0,1,1,1), how do I pass this design to MTP?