The road after DESeq2 vs edgeR vs Cuffdiff results

[sindrle]

Hi!
After great help from the community, special thanks to dryan, Simon Anders and Michael Love, I know have my comparison of edgeR, DESeq2 and Cuffdiff.

For the interested:

Different treatment effect on groups Treatment effect Group effect
DEseq2 0 85 4500
edgeR 0 600 4006
Cuffdiff NA 199 1890

The question is; where does the road go from this?

Im thinking taking the intersect, making Venn diagram, maybe qPCR, GAGE analysis?

Thanks!