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  • Trudy
    Member
    • Feb 2011
    • 16
    #1

    Cufflinks quantification and Cuffdiff output

    Hello!!!

    I used Cufflinks for quantification and for differential expression analysis but I have an important question:
    I obtained FPKM quantification values for each sample like this:
    tracking_id FPKM1 FPKM2 FPKM3
    XLOC_000007 1.19211 0.858113 1.06576


    but when I compare this 3 sample with Cuffdiff the relative FPKM value are very different and higher
    tracking_id FPKM1 FPKM2 FPKM3
    XLOC_000007 311.493 276.814 230.429

    why?
    Tags: None
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