[BioC] Time-point analysis

[Narendra Kaushik]

I am comparing gene expression profile in animal model at different time point: 

Animals                                       Age 
WT                                             400 
Trans                                         400 
WT                                            700 
Trans                                         700 
WT                                            800 
Trans                                         800

All experiments are perfomed with 3 biological replicates in each group with Affy chips. I am
looking for differentially expressed genes in each groups as well as dynamics of gene profiles in
all groups, e.g how genes A......Z  are expressed in all groups.
What is the best way to analyse this type of experiments and which package is suitable. 

Thanks in advance

Narendra