Update diagnosis and disease timing numbers #133
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| The largest number of samples found on the Portal were obtained from patients with leukemia (n = 216). | ||
| The Portal also includes samples from sarcoma and soft tissue tumors (n = 194), brain and central nervous system tumors (n = 167), and a variety of other solid tumors (n = 117). | ||
| Most samples were collected at initial diagnosis (n = 521), with a smaller number of samples collected either at recurrence (n = 129), during progressive disease (n = 13), during or after treatment (n = 11), or post-mortem (n = 5). | ||
| Along with the patient tumors, the Portal contains a small number of human tumor cell line samples (n = 6). |
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So, only the 4 NB cell lines are marked as cell lines on the Portal. The PDX lines (https://scpca.alexslemonade.org/projects/SCPCP000024) are marked as PDX. I see your point here, but we should either be consistent with the Portal or perhaps set is_cell_line and is_xenograft both to TRUE.
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Ah okay I was confused about this because I thought we had 6 cell lines, but then when I looked at the portal there was only 4 and then I filtered our sample metadata by is_cell_line and only saw 4. I think that they should both be set to true.
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If you're good with that, then I'll file an issue to update that in ScPCA-admin and group that with the other metadata changes for hand off and then update the number here to 6.
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Yea, that's fine. In practice, we should bundle updating this with the other data release 🎟️
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You said that already. I missed it.
allyhawkins
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…ase-timing-number-update [ci skip] This build is based on 6c5de76. This commit was created by the following CI build and job: https://github.com/AlexsLemonade/ScPCA-manuscript/commit/6c5de76828f424fe5c6dfcf1f050e992c6f659ad/checks https://github.com/AlexsLemonade/ScPCA-manuscript/actions/runs/12771424391
…ase-timing-number-update [ci skip] This build is based on 6c5de76. This commit was created by the following CI build and job: https://github.com/AlexsLemonade/ScPCA-manuscript/commit/6c5de76828f424fe5c6dfcf1f050e992c6f659ad/checks https://github.com/AlexsLemonade/ScPCA-manuscript/actions/runs/12771424391
Closes #124
Here I'm just updating the text to have the updated numbers for diagnoses and disease timing. The updated numbers are from the tables in
scpca-paper-figures.I also found a spot in the legend that needed to be updated based on the new numbers.