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  • mrbirdy857
    Junior Member
    • Jan 2012
    • 3
    #1

    Cufflinks FPKM Confidence Intervals--Sources of Variability

    Hello,

    Based on the original Cufflinks paper (Nat. Biotech), it would seem that two types of variability are associated with the FPKM measure for a particular transcript (A_t): (i) count variability for the locus (from X_g) and (ii) isoform fraction variability (from gamma_t). Does anybody know if the confidence interval reported by cufflinks incorporates these two types of variability? Or does it only reflect the uncertainty in isoform fraction (gamma_t)?

    Also, is this confidence interval based on the normal distribution?

    Thanks for any help.
    Tags: None
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