Hi! Scanpy community,
I am still learning Scanpy based on my experience with Seurat. and I would like to know some answers of the following questions.
How can I get access with the raw count matrix of anndata object?
I tried with adata.raw, but it looked like the normalized data.
If I want to integrate two already analyzed anndata from two different studies. What’s the proper steps for doing that?
Just concatenate these two adata and do PCA and integration workflow like Harmony, then Umap?
Or should I normalize them again? And this brings me to the first question, because I don’t know where to find the raw data.