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.
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.