Ben Parks

Hi @plbngl, thanks for the issue report! To clarify -- have you been able to run this approach successfully on another dataset, or does it always have the same problem?...

Hi @plbngl, thanks for providing the test script to run on the pbmc3k demo dataset! I tried re-running your example but I got different results. How recently have you re-installed...

Okay, that's helpful to know. My first instinct is to look closer at how BPCells was installed. Did you install BPCells from the r-bpcells bioconda package or using `remotes::install_github("bnprks/BPCells/r")` from...

Perfect, glad that fixed your problem! It sounds like we should look into why the conda version has this bug and maybe tag a new release so that the conda...

Just chiming in here as a BPCells author: the functionality to regress out data with a linear model does exist in BPCells via the function [`BPCells::regress_out()`](https://bnprks.github.io/BPCells/reference/regress_out.html). So if Seurat's `ScaleData.IterableMatrix`...

Hi @nashchem, sorry for the slow response here. Would you be able to provide more background on exactly what you ran to prep the seurat object you used? Just the...