[BioC] which genes to choose for being truly differentially expressed from a long list

[EJ [guest]]

Dear All,
I used LIMMA for a dataset on Human plus 2.0 arrayto get fold change values for differentially expressed genes. I have a long list of 500 some genes with fold changes > 2 from the topTable function. How can I select genes which are most differentially expressed from this list?

Thank you,
EJ

 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252   
[3] LC_MONETARY=English_India.1252 LC_NUMERIC=C                  
[5] LC_TIME=English_India.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] limma_3.16.7       affy_1.38.1        Biobase_2.20.1     BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] affyio_1.28.0         BiocInstaller_1.10.3  preprocessCore_1.22.0
[4] zlibbioc_1.6.0 

--
Sent via the guest posting facility at bioconductor.org.