How to use the VisiumHD (sketch-based clustering) vignette + the scRNA-seq (multi-sample sketch-based cluserting + integration) vignette together (question about a small difference)?

[Pancreas-Pratik]

I have two VisiumHD datasets (one is treatment and the other is control of the same tissue).

The 2 vignettes I am using:

1. the VisiumHD sketch single-sample vignette (https://satijalab.org/seurat/articles/visiumhd_analysis_vignette#unsupervised-clustering-mouse-intestine) uses sketch-based clustering but the vignette is only with one sample

2. there is a scRNA-seq sketch multi-sample integration vignette (https://satijalab.org/seurat/articles/parsebio_sketch_integration) that uses multiple samples, but with scRNA-seq data (not Visium)

---

My question is about a small difference in these two vignettes:

• In the VisiumHD sketch single-sample vignette there is a ScaleData() step prior to the SketchData() step, however in the scRNA-seq sketch multi-sample integration vignette this step is not present.

Is there a reasoning for doing it this way in the VisiumHD sketch single-sample vignette, but not in the scRNA-seq sketch multi-sample integration vignette?