pbmc68k_reduced raw counts
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Description
Hi!
I was playing with the pbmc68k_reduced dataset and I saw that it has decimal values even in the "raw" matrix:
>>> adata.raw.X.data
array([2.177, 2.177, 2.544, ..., 1.142, 2.255, 1.142], dtype=float32)
which transformation has been applied? shouldn't the "raw" group contain unprocessed counts? is there a standard for this? Ideally, I would like to know where to find the raw, unprocessed, counts everytime I see an anndata or h5ad file.
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First steps
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Research direction
Start with the scanpy.datasets.pbmc68k_reduced documentation linked in the issue and inspect how its adata.raw.X values are produced. Determine which transformation was applied, whether raw has a defined standard, and document where users can find unprocessed counts in an AnnData or h5ad file.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, data
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100