I am having difficulty understanding the comparison between conditions in the design formula created for an analysis with DRIMSeq.

Basically, I have 3 conditions: Healthy, Not_healthy1, Not_healthy2. My purpose is to feed the model comparing Healthy vs Not_healthy1 and Healthy vs Not_healthy2 (separately), but I am confused about the design formula. I created it with the following code, with `-1`

indicating no intercept:

```
design_full <- model.matrix(~ -1 + condition, data=DRIMSeq::samples(d))
```

The design formula is this one:

```
Not_healthy1 Not_healthy2 Healthy
P1 1 0 0
P2 1 0 0
P3 0 0 1
P4 1 0 0
```

The next step for the analysis will be this one:

```
set.seed(1)
system.time({
d <- dmPrecision(d, design=design_full)
d <- dmFit(d, design=design_full)
d <- dmTest(d, coef="Healthy")
})
```

How can I set as baseline the condition `Healthy`

and compare that to the others exclusively ? I think that in this way I am comparing `Healthy`

versus al the others, that is not correct for my purposes.

I don't know the DRIMseq package, but basically you have two options. Either use a design without intercept (~0+group) and then use contrasts or with an intercept and make sure that group is a factor and the reference level is the group level you want to compare against.