Right assay and slot for the extraction of normalized data after "sct normalization" and "anchor based integration"

Question

[Omics data mining]

Hello everyone

I am using Seurat for single cell data analysis. I used SCTransform for normalization follows by anchor based integration method for integration of multiple samples. Now I want to extract "normalized count" from seurat object. I can find multiple assays :

1) Integrated assay

2) RNA assay

I used RNA assay for differential analysis as recommended in seurat tutorials.

Next, I want to extract normalized data or log-transformed data (across all samples). I am not sure about the right assay and slot.

which assay should I use between "integrated" or "RNA" for normalized count and under which slot "counts", "scale.data", "data" ?

I would appreciate all suggestions.

Thanks in advance

[jv]

the integrated assay will only include the integration anchor genes. You should however also have an SCT assay which will include "count" and "data" slots and I think that's the assay you are interested in.