**780**wrote:

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

**520**• written 8.8 years ago by Israel Barrantes •

**780**

In common with the 2 answers so far, I don't understand the question. Could you add some additional information or consider re-wording it, because I'm not sure it's answerable in its current form.

13kHere it's the question, posed in a different way:

We have the read counts of two samples, X and Y, for each different transcript available.

The question is now the following: Give me a list of all transcript names, the true expression level of which is, with 95 % confidence, at least 5-fold different in the two samples.

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

780Ah, I see. This is something i have been asking myself for a long time, but I don't have a solution. I will keep watching this thread...

2.3kI edited the question accordingly.

780