**10**wrote:

Hi everyone,

I have miRNA-Seq data for an experiment with the following parameters:

SampleID Treatment Timepoint Patient

P1_0 TB 0 1

P1_1 TB 1 1

P1_2 TB 3 1

HC1_0 None 0 Control1

HC1_2 None 3 Control1

P2_0 TB 0 2

P2_1 TB 1 2

P2_2 TB 2 2

P2_3 TB 3 2

HC2_0 None 0 Control2

HC2_3 None 3 Control2

I am really struggling figuring out how to enter the design formula. There are 2 patients each with a baseline sample before treatment and 2 samples at time points after treatment. Each patient has an age-matched control with samples taken at two time points. One patient is a full responder to treatment and one is not but I am blinded to that info. The investigator wants to identify DEmiRNAs in the following:

1. Between patients

2. As a result of treatment over time

Do I need to include interaction terms? So far I have identified 128 DEmiRNAs using this formula:

`design=~timepoint + individual`

`Which I believe is testing for differences between individuals across all time points, can anyone provide some much needed guidance?`

**20**• written 22 months ago by gkuffel •

**10**