[BioC] negative correlation?

[Naomi Altman]

I am running limma 2.8 on a technical replicate dye-swap 
design.  Here is my design matrix:

(Intercept) as.factor(targets$time)24h as.factor(targets$time)4h 
as.factor(targets$time)8h
1           -1                          0                         0 
                       0
2            1                          0                         0 
                       0
3           -1                          0                         0 
                       0
4            1                          0                         0 
                       0
5           -1                          0                         1 
                       0
6            1                          0                         1 
                       0
7           -1                          0                         1 
                       0
8            1                          0                         1 
                       0
9           -1                          0                         0 
                       1
10           1                          0                         0 
                       1
11          -1                          0                         0 
                       1
12           1                          0                         0 
                       1
13          -1                          1                         0 
                       0
14           1                          1                         0 
                       0
15          -1                          1                         0 
                       0
16           1                          1                         0 
                       0


corfit <- duplicateCorrelation(MA, design=designTimeR,ndups = 1, 
block = targets$biorep)

targets$biorep
  [1] 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8


 > corfit$con
[1] -0.3414428

Why am I getting a negative correlation between bio reps?  Is this 
expected due to the dye swap?

--Naomi