Christoph Hafemeister

What are the dimensions of your input matrix? What are the exact commands you use? It's hard to pinpoint the issue without that information. If you are using `Seurat::SCTransform` you...

Do all input cells have at least one count? Please provide the exact steps to reproduce the problem.

`sctransform::vst` makes some basic assumptions about the input data. The error message mentioned above suggests that either the input umi matrix was not made up of non-negative counts, or there...

@smaniatis I would need the data to figure out what exactly the problem is. If you share the exact commands you used and the input (.h5 file or counts matrix)...

Hi Andrei, Yes, you are right, thank you for bringing it up. I had I run into this problem (again) recently. The problem is also described here https://github.com/RfastOfficial/Rfast/issues/5 I will...

Hi, I cannot comment on your specific results without actually seeing them and understanding why you think sctransform normalization does not lead "to a correct clustering of the spots". But...

I agree that it would be awesome, but so far this feature has only been tested in a previous development version of sctransform (through [loomR](https://github.com/mojaveazure/loomR)). I will look into the...

No, sctransform does not account for changes in the RNA composition. However, I don't think compositional effects are that strong between non-activated and TCR-activated T cells. Compositional bias is more...

Yes, looks like there was an error. I'm going to need more information than that screenshot to identify the problem. Can you provide a [minimal reproducible example](https://www.dummies.com/programming/r/how-to-make-a-minimal-reproducible-example-to-get-help-with-r/)?

Hi Alex, I cannot comment since I have not had a chance to look at Spatial Transcriptomics data. But I'd assume that it looks quite different from droplet based UMI...