docs: clarify source-defined expression representations

CHANGELOG.md

@@ -9,3 +9,11 @@ The versioned release contains 4,468 sample packages from 507 GEO studies. Packa
 Publication adds the dataset card, versioned sample/study indexes, schema and coverage summaries, archive checksums, a nine-sample tissue/QC preview, usage documentation and executable download/verification/split examples. Broken path concatenations in the draft card are corrected. Viewer configurations refer only to the selected Parquet files, and the size tag describes the 4,468-row catalog rather than the number of expression observations.
 
 All remote package LFS SHA256 values and sizes are reconciled against the release manifest. Anonymous clean-cache download, archive/member integrity, H5AD loading, image access and Hub Viewer checks are recorded separately in publication receipts. The release does not reinterpret review labels, remove source-verification annotations, change matrices/images, or squash repository history.
+
+## 2026-09-17-v1.2
+
+- Documentation-only clarification of expression representation.
+- Explicitly lists eight samples with clearly non-integer `X` values.
+- Clarifies that HESRT preserves source-defined expression matrices and does not infer or synthesize raw counts.
+- No sample payload, catalog row, image, expression matrix, checksum, or release namespace changed.
+

README.md

@@ -114,7 +114,7 @@ GSM....tar.zst
   manifest.json              Per-member sizes and SHA256 hashes
 ```
 
-Expression/image binaries are unchanged by lossless packaging of the selected standardized artifacts. This does not imply all expression matrices contain raw UMI counts or that the upstream standardization left original GEO files unchanged. Coordinate frame, units and expression representation should be interpreted using provenance. The name `wsi.tif` does not guarantee a TIFF file, a specific stain, or a full-resolution whole-slide scan.
+Expression/image binaries are unchanged by lossless packaging of the selected standardized artifacts. HESRT does **not** claim that every `X` matrix contains source-verified raw UMI counts. A release-wide numerical audit identified eight samples whose `X` matrices contain clear non-integer values: `GSM7781044` (GSE243225) and `GSM8243007`–`GSM8243013` (GSE266244). These source-defined matrices are retained as deposited/standardized rather than reverse-engineered into synthetic counts. Analyses that require integer raw counts should exclude or source-verify these eight samples. The remaining matrices are integer-typed or numerically integer-like in the audit, but that alone is not proof of raw-count provenance. Coordinate frame, units and expression representation should be interpreted using provenance. The name `wsi.tif` does not guarantee a TIFF file, a specific stain, or a full-resolution whole-slide scan.
 
 ## Release files
 
@@ -124,4 +124,4 @@ For evaluation, keep studies and shared content together, resolve donor/cohort o
 
 ## Reuse and citation
 
-Underlying source materials retain their source-specific terms; no blanket redistribution license is asserted. Cite the source GEO accessions/publications and **HESRT release 2026-09-17-v1.1**, recording its resolved Hub commit. See [reuse and citation](docs/REUSE.md) and [release notes](CHANGELOG.md). This resource is intended for research, not clinical decision making.
+Underlying source materials retain their source-specific terms; no blanket redistribution license is asserted. Cite the source GEO accessions/publications and **HESRT release 2026-09-17-v1.2**, recording its resolved Hub commit. See [reuse and citation](docs/REUSE.md) and [release notes](CHANGELOG.md). This resource is intended for research, not clinical decision making.

docs/KNOWN_ISSUES.md

@@ -13,3 +13,7 @@ Expression and image binaries are byte-identical to the selected standardized in
 The `wsi.tif` member can contain a different image format, including JPEG, and some sources provide only reduced-resolution images. Coordinate fields are indexed, but their units and image frame must be read from provenance. Do not infer stain, physical resolution, cell identities or registration quality from filenames or thumbnail appearance.
 
 Visual previews are nine deliberately selected examples spanning tissues and platform labels. They are **not a random sample**, a quality leaderboard, a new alignment audit, or a representative estimate of cohort composition. Tissue images and pre-existing QC graphics were downsampled from the released packages. Display transformations and source hashes are recorded in `assets/preview_manifest.json`. No source matrix or image is modified by generating previews.
+## Source-defined expression matrices
+
+HESRT preserves the expression representation carried by the selected standardized artifact; it does not globally re-normalize expression. A numerical audit of release 2026-09-17 identified eight samples with clearly non-integer values in `X`: `GSM7781044` (GSE243225) and `GSM8243007`, `GSM8243008`, `GSM8243009`, `GSM8243010`, `GSM8243011`, `GSM8243012`, `GSM8243013` (GSE266244). These matrices were not rounded or reverse-transformed. Exclude or source-verify them for analyses that assume integer raw counts. Integer-valued matrices elsewhere in HESRT are not automatically certified as raw UMI counts.
+