In RNA-seq and other gene expression approaches, usually you calculate the probability of obtaining a Y value (measured in sample B) from X (sample A), such in the case discussed by Audic and Claverie (Genome Res. 1997 Oct;7:986).
Now the case is the following: Having the read counts of two samples (X and Y, for each different transcript available), we would like to obtain a list of all transcript IDs, the true expression level of which is, with 95 % confidence, at least 5-fold different in the two samples. Which statistical test could help in this case?
Certainly, we would like to choose between 95% and 99% confidence intervals and betwees arbitrary cut-offs of x-fold expression, receiving e.g. a list of all transcripts that are 2-fold or 20-fold or 100-fold overexpressed at the choosen error probability p < given value