Chananchida Sang-aram

Hi, Did you try already running PrepSCTFindMarkers() prior to running the code above, as suggested by the error message?

What happens when you run `FindMarkers` on your object? `get_lfc_celltype` uses `FindMarkers` internally, so could you try running this (assuming that the `Idents()` of your object is the celltype)? `FindMarkers(seuratObj,...

I just recalled that to fix this issue, you should set `recorrect_umi = FALSE` in `FindMarkers()`: https://satijalab.org/seurat/archive/v4.3/sctransform_v2_vignette > If running on a subset of the original object after running [PrepSCTFindMarkers()](https://satijalab.org/seurat/archive/reference/PrepSCTFindMarkers.html),...

However, `get_lfc_celltype` currently doesn't allow you to pass extra parameters into `FindMarkers`. You can reproduce the results of `get_lfc_celltype` with something like this: ``` lapply(Idents(seuratObj) %>% levels() %>% intersect(sender_celltypes), function(ct)...

[`get_lfc_celltype`](https://github.com/saeyslab/nichenetr/blob/dd7a859b2388786159f66ee3abe0abf137a98f8d/man/get_lfc_celltype.Rd) now allows you to pass extra arguments to `FindMarkers`

Hi, @shayansaniei @wanwan26 Can you try following my suggestion from #253 to see if you can follow the classical pipeline? I'm aware that there's currently an issue with the wrapper...

If you update to NicheNet v2.0.6, the wrapper function should also work with v5 objects now.

@bschilder @rcannood By the way, I will not have time to work on this anymore before the deadline. You can see what I've done so far in the `issue-60-from-seurat-obsm-varm` branch....

Hi @Boehmin, Please refer to #258 for the solution.

Could you try following the step-by-step analysis instead and see if you can run the vignette? https://github.com/saeyslab/nichenetr/blob/master/vignettes/seurat_steps.md In the meantime I'll try to fix the issue in the coming weeks.