Hi,
I’m a fresh guy in processing CITE-seq data and so glad to see such a wonderful framework for multimodal data.
I only had filtered data, so I chose CLR normalization for my ADT matrix. However, I was confused about whether I should do scaling before running PCA DR. Because I had read the Seurat pipline for WNN before, and scaling was performed before PCA in that pipline(see the link: Analysis, visualization, and integration of Visium HD spatial datasets with Seurat • Seurat).
Could anyone give some advice? I would be so appreciated.