Hi,

I am analyzing a set of 10 dual-labelled cDNA arrays to study the effect of
overexpressed gene X over two time points at 8h and 16h. The gene X is
transfected with plasmid PT into the cell-line CL. The arrays follow a
common reference design with dye-swap. Their details are

     Array
 Description
 Cy5
 Cy3
 1
 Total RNA of cell line at time 0h
 CL
 UHR
 2
 Total RNA of cell line at time 0h
 UHR
 CL
 3
 Total RNA of cell line transfected with empty plasmid at time 8h
 PT
 UHR
 4
 Total RNA of cell line transfected with empty plasmid at time 8h
 UHR
 PT
 5
 Total RNA of cell line transfected with plasmid containing gene X at time
8h
 X
 UHR
 6
 Total RNA of cell line transfected with plasmid containing gene X at time
8h
 UHR
 X
 7
 Total RNA of cell line transfected with empty plasmid at time 16h
 PT
 UHR
 8
 Total RNA of cell line transfected with empty plasmid at time 16h
 UHR
 PT
 9
 Total RNA of cell line transfected with plasmid containing gene X at time
16h
 X
 UHR
 10
 Total RNA of cell line transfected with plasmid containing gene X at time
16h
 UHR
 X

I am interested to study the effect of gene X on the transcriptome at 8h and
16h. What methodology should I adopt to process the data to get the list of
differential expressed genes at 8h and 16h ?

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