const-ae / const-ae/proDA

different results for some proteins depending test used.

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Description

Hi Constantin,

A Question:

I am running two tests with proDA, once the LR and once the Wald test.
The data is a repeated measurement on 5 subjects with two groups (high and low)

I would think that the two tests are equivalent. However, for a group of proteins, I am getting substantially different results.
Can you have a look at my code, please? Is the difference in p-values within the range you would expect, and what is the explanation for it in your opinion?

```
fit <- proDA(se, design = ~ group_ + subject_, data_is_log_transformed = TRUE)
lrTest <- test_diff(fit, reduced_model = ~ subject_)
fit2 <- proDA(se, design = ~ group_ + subject_ - 1, data_is_log_transformed = TRUE)
waldTest <- test_diff(fit2, group_high - group_low)
lrT <- select(lrTest, name, adj_pval)
wT <- select(waldTest, name, adj_pval)
tmp <- inner_join(lrT, wT, by = "name", suffix=c("lr.Test","wald.Test"))
plot(tmp$adj_pvallr.Test, tmp$adj_pvalwald.Test)
```

![image](https://user-images.githubusercontent.com/1926513/163347775-0a55803b-51b5-4508-8917-d6b1875bf1b8.png)

best regards
Witold

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