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How to do data preprocessing? #4

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caoname opened this issue Nov 13, 2024 · 0 comments
Open

How to do data preprocessing? #4

caoname opened this issue Nov 13, 2024 · 0 comments

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@caoname
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caoname commented Nov 13, 2024

According to tutorial 1, does hbc-G2 set These three are combined into one .h5ad file, ()? There is also the HCC-V05.H5AD file that has been downloaded, but there is no batch column in his obs, may I ask how this batch comes from?
According to Tutorial 1, hbc-G2 is not going to combine these three {1) gene expression matrix in adata.X; 2) spatial coordinates in adata.obsm['spatial']; 3) histology image in adata.uns['spatial'].} into a.H5ad file, but if you process these three files, how can I ensure that the data structure is the same as in the tutorial (To make the model can read the data sucessfully, please ensure the same anndata structure as example.)? There is also the HBC-V05.h5ad file that has been downloaded, but there is no batch column in his obs, may I ask how this batch comes from?
I would appreciate it if you could answer my questions

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