input data processing

[vravik]

Dear Wei Liu,

I was wondering if there is any pre-processing we must do for the visium datasets before integration using Precast. The paper says you assume a centered normal distribution, so do you require us to normalize and scale the input data before creating the precast object?

Also, are the counts from the integrated seurat object created by precast normalized for variations in library size between the slides?

Thank you, Best, Vish

[feiyoung]

Hi Vish, Please refer to the package website for more tutorials: https://feiyoung.github.io/PRECAST/index.html.