mhkowalski

Hi, Could you try running the function for CellCycleScoring _before_ you subset out your cells of interest? As the other issues mention, this function does not work well when many...

Hello, Are you able to run these functions using the data in the [vignette](https://satijalab.org/seurat/articles/integration_mapping.html)? If so, there is something likely going on when you are finding anchors between your query...

Hi, I agree with Sam's comments and that ```FeaturePlot``` may not be the visualization to compare the percentage of cells expressing a certain gene, as ```VlnPlot``` and ```DotPlot``` may be...

Hello, Please see [this issue ](https://github.com/satijalab/seurat-object/issues/165). The ```.GetSeuratCompat()``` function was released in `SeuratObject` version 5, so there might be a problem with multiple version installations.

Hello, Also linking our [NEWS](https://satijalab.org/seurat/articles/announcements.html) page that describes this change. The difference is related to choice in pseudocount, which will be much higher for lowly expressed genes.

Closing this issue, please open a new issue if anyone is encountering difficulties with installing the latest version of Seurat.

Hello, What version of Seurat are you running? It's possible this may be an old version.

Do you mean tools that provide annotation predictions, like our [Azimuth](https://azimuth.hubmapconsortium.org/) tool? I would recommend performing prediction separately for each "batch", rather than trying to used the corrected counts.

Hello, Thanks for your question. I wouldn't recommend calculating fold changes from aggregated counts in a pseudobulk object, as this might be confounded by how many cells (and how deeply...

Thanks for reporting this. This is all fine. We're working on fixing this so the warnings won't come up, but this should not affect your results.