[BioC] Designing a model matrix in limma for 4 conditions x 2 colors

[Matthew Vaughn]

I am analyzing in limma a two-color array experiment where I am  
compare 4 conditions: Wild-type (WT) versus Knock-out (KO) x Normal  
(NORM) versus Stress (STRESS). The hybs are replicated once  
(NNNNN_BLOCK1 and NNNNN_BLOCK2). I am most interested KOSTRESS-KONORM  
relationship for all genes on the array but would like to do all  
possible comparisons for my own reference. However, and I am sure  
this is due to a limitation of my intellect, I cannot figure out how  
to construct a design object to accomplish this. If the arrays shared  
a common reference (WT-ONLY), I would just do 'design <- modelMatrix 
(targets,ref="WT-ONLY")' but this is more complicated. Can someone  
please enlighten me? The content of the  targets file for this  
experiment is at the end of this message.

Thank you,

Matt Vaughn

FileName	Cy5	Cy3
90930_BLOCK1.dat	WTNORM	KONORM
90930_BLOCK2.dat	WTNORM	KONORM
91003_BLOCK1.dat	WTSTRESS	KOSTRESS
91003_BLOCK2.dat	WTSTRESS	KOSTRESS

--
Matthew W. Vaughn, Ph.D.
Scientific Informatics Analyst
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

phone: (516) 367-8469