mikessh Claude Opus 5 commited on
Commit
82dd501
·
1 Parent(s): d0312b1

expression/SOURCES.md: the prose still said two sources

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Adding hpa_consensus left the surrounding text stale -- "two references", "both sources
are measured RNA-seq", a key_type paragraph naming only GTEx and TCGA, and a ~105 MB
download size for a file that is now larger. Found by auditing every count claimed in the
published docs against the files themselves; the counts were right, the prose around them
was not.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

Files changed (1) hide show
  1. expression/SOURCES.md +8 -7
expression/SOURCES.md CHANGED
@@ -1,14 +1,14 @@
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  # `expression/` — sources
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- One file, two references that are **never merged** — different measurements, different units, and a
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- gene-keyed table and a peptide-keyed one are not the same object.
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  | | |
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  |---|---|
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  | file | `reference_expression.tsv.gz` |
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  | rows | 6,681,814 |
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  | schema | `key`, `key_type`, `source`, `context`, `median_tpm`, `q25_tpm`, `q75_tpm`, `n` |
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- | provenance | **experimental** (both sources are measured RNA-seq); the per-context median/IQR/`n` are **computed** summaries of it |
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  | `source` | `key_type` | rows | contexts | what a row is |
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  |---|---|--:|--:|---|
@@ -18,12 +18,13 @@ gene-keyed table and a peptide-keyed one are not the same object.
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  Total 6,681,814 rows.
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- `key_type` is the join key and it differs by source on purpose: GTEx answers "is this gene on in
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- normal tissue", TCGA answers "is this neoantigen transcribed in this tumour". A caller that treats
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- them as one column is asking a question neither answers.
 
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  Read through `mhcmatch.expression` (`lookup`, `tissues`, `tumor_types`, `safety_profile`), which
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- keeps the two apart. Fetched by `mhcmatch bootstrap --reference` (~105 MB).
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  ---
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  # `expression/` — sources
2
 
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+ One file, three references that are **never merged** — different measurements, different units, and
4
+ a gene-keyed table and a peptide-keyed one are not the same object.
5
 
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  | | |
7
  |---|---|
8
  | file | `reference_expression.tsv.gz` |
9
  | rows | 6,681,814 |
10
  | schema | `key`, `key_type`, `source`, `context`, `median_tpm`, `q25_tpm`, `q75_tpm`, `n` |
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+ | provenance | **experimental** (all three sources are measured RNA-seq); the per-context median/IQR/`n` are **computed** summaries of it |
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  | `source` | `key_type` | rows | contexts | what a row is |
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  |---|---|--:|--:|---|
 
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  Total 6,681,814 rows.
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+ `key_type` is the join key and it differs by source on purpose: GTEx and HPA answer "is this gene on
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+ in normal tissue", TCGA answers "is this neoantigen transcribed in this tumour". A caller that treats
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+ them as one column is asking a question none of them answers. GTEx and HPA are both gene-keyed but
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+ are still not interchangeable — see the units caveat in the HPA section below.
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  Read through `mhcmatch.expression` (`lookup`, `tissues`, `tumor_types`, `safety_profile`), which
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+ keeps them apart. Fetched by `mhcmatch bootstrap --reference` (~115 MB).
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  ---
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