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  • The road after DESeq2 vs edgeR vs Cuffdiff results

    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!

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