[BioC] Packages for differentially expressed genes

[Peter Kupfer]

Dear all,
first time for my to work with steady state data. Two groups and 30 arrays (hgu133a- arrays) in total. In the past I worked with time course and/or limma to detect differentially expressed genes. Are there any packages which you would recommend for the detection of differentially expressed genes?
Would be nice if I get some new inputs. 
All the best
Peter