Add remaining text to spatial 01 notebook#957
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sjspielman merged 7 commits intomasterfrom Mar 24, 2026
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…hroughout document
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allyhawkins
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LGTM, just one comment about normalization. I agree that we should be upfront about the caveats you mention, but I do think we are going to get a lot of questions. I don't know that we really know the answer to them though.
spatial/01-spatial_intro.Rmd
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| It's worth noting this approach doesn't take spatial information directly into account; there are some approaches out there which account for spatial information, but this aspect of analysis seems to be pretty in flux. | ||
| Also, bear in mind the caveat that in some cases library size itself is [also confounded with spatial structure](https://link.springer.com/article/10.1186/s13059-024-03241-7); so, keep your eyes peeled for normalization developments, since this space is evolving rapidly. | ||
| It's important to note that this approach doesn't take spatial information directly into account, although there are [some proposed methods](https://bioconductor.org/books/3.22/OSTA/pages/seq-intermediate-processing.html#spatially-aware-normalization) which do. | ||
| It's just as important to note that the normalization approach we're using here could also be problematic, as there's some evidence that library size itself [can be confounded with spatial structure](https://link.springer.com/article/10.1186/s13059-024-03241-7). |
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I think it's good to be transparent about this, but we are going to get a lot of questions about why we are normalizing if this is the case, so we should be prepared to answer those...
Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
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Closes #946(woopsies branch name; this is already closed)Closes #947
Closes #948
This PR wraps up the text for our first notebook! Changes include: