Constantin

Hi M, thanks for your interest and reaching out. > I would expect at least some separation based on the conditions (since for some of them the pseudo-bulk results are...

> Btw. is there a way to limit the memory of the lemur function call? It is very fast but super memory intesive. Ideally, I don't always need to run...

Hey, I would recommend fitting a single model (e.g., `design = ~ condition`), and then in the contrast, you will need to compare pairs of conditions (e.g., `test_de(..., contrast =...

> my question mainly arose because after fitting and performing DE on pairs of conditions the way you said, i get stuck at finding de neighborhoods: Ah, I see. Do...

> Are two independent samples per timepoint and condition enough to run lemur? The answer of course depends on the magnitude of the expression changes. But if you have enough...

Hey, thanks for reporting the issue. I assume that you are using `glmGamPoi` version 1.9 or 1.10? `lemur` is using the `pseudobulk` function from `glmGamPoi` which I only added recently...

Sorry for the tedious experience and thank you so much for giving my packages a try. This is really valuable feedback that will hopefully make things easier for everyone in...

Hi shobhit, thank you :) To fit a multi-subject two-condition analysis, set the design to `~ condition` (i.e., drop the subject). This fits a single coefficient explaining the treatment effect...

Yes. The way the replicates are specified is through the `group_by` argument in `find_de_neighborhoods`. Here you would set `group_by = vars(subject, condition)`.

Hi Minhui, I would expect that some methods have no problem handling such a large dataset (e.g., log, acosh). In contrast, others perform much more demanding computations and will need...