[BioC] How to carry out time series analysis in Bioconductor

[yemi yomi]

Hello All
I'm having difficulties carrying out a time series analysis of my dataset using Bioconductor! Could anyone help me out in this area:

I have microarray time course data for 1hr, 2hr, 3hr and 4hr time points:

Treatment                  

E1H1                      
E1H2  =A                
E1H3

E2H1
E2H2  =B
E2H3

E3H1
E3H2  =C
E3H3

E4H1
E4H2  =D
E4H3 

pooled Control dataset
R1H1
R2H2
R3H3 =E
R4H4

the design matrix is such that I compared each total replicate in the treatment i.e A, B, C, and D with E. Thus

A is compared with E
B with E
C with E
and D with E

Using BH method in LIMMA analysis how do I carry out a time series analysis of this time course data?
Any useful suggestions in the area of matrix design and useful codes would be greatly appreciated.

Yemi
PhD student