[BioC] LIMMA package differentially expressed genes

[Prasad Siddavatam]

I am kind of new to Gene expression studies.

I have two questions.
1. What would be the design matrix for reference design with dye-swap time 
course experiment. I have 6 time points and at each time point, I have dye-swaps 
and 3 replicates for infection and control samples (A total of 12 samples at 
every time point). What I want is the differentially expressed between control 
and infection.


2. In other set, I have to make multiple comparisons (infection1, infection2, 
infection3). This is also a reference design with two-colors. 
sample    cy3    cy5
array1      ref    inf.1
array2      ref    inf.1
array3      ref    inf.1
array4      ref    inf.2
array5      ref    inf.2
array6      ref    inf.2
array7      ref    inf.3
array8      ref    inf.3
array9      ref    inf.3
array10     ref    control1
array11     ref    control2
array12     ref    control3
what I want is differentially expressed genes between every pair of comparisons 
(ex. inf1-inf2). 
my design looks like this
            inf1    inf2   inf3    control
array1      1        0       0       0
array2      1        0       0       0
array3      1        0       0       0
array4      0        1       0       0
array5      0        1       0       0
array6      0        1       0       0
array7      0        0       1       0
array8      0        0       1       0
array9      0        0       1       0
array10     0        0       0       1
array11     0        0       0       1
array12     0        0       0       1

what would be my contrast matrix would be?
and how to get the genes between inf2 and inf3?

Prasad siddavatam