[BioC] help with design matrix

[Dennis Hazelett]

Hello Everyone,
I am trying to compare two red-labeled samples via a green-labeled 
reference RNA. Here is an example of a script I've run:

 > library(limma)
 > files <- dir(pattern="*.gpr")
 > RG <- read.maimages(files, source="genepix")
Read 099.gpr
Read 101.gpr
Read 105.gpr
Read 107.gpr
Read 111.gpr
Read 113.gpr
 >
 > targets <- readTargets()
 > targets
  FileName Cy3 Cy5 Name
1  099.gpr Ref  A3   99
2  101.gpr Ref  A5  101
3  105.gpr Ref  A3  105
4  107.gpr Ref  A5  107
5  111.gpr Ref  A3  111
6  113.gpr Ref  A5  113
 >
 > RG$genes <- readGAL()
 > design <- designMatrix(targets,ref="Ref")
 > design
  A3 A5
1  1  0
2  0  1
3  1  0
4  0  1
5  1  0
6  0  1

My intention is to compare "A3" with "A5" via a common reference, "Ref", 
similar (I think) to the example in the limma User's guide section 8.2 
"ApoAI Knockout Data ...". What am I doing wrong? Is my Targets.txt file 
set up incorrectly? In its current state it results in topTable giving 
me a list that seems appropriate for contrast between Cy3 and Cy5. I've 
also tried creating a "design" object like the one in the example 
manually by writing it in a text editor and importing it with 
read.table(). I just get nonsense back from that.

I'm running BioC v1.3 R 1.8.1 on linux kernel 2.6.4

Thanks in advance for the help.

-Dennis