Paper · S7563
Joint Modeling and Registration of Cell Populations in Cohorts of High-Dimensional Flow Cytometric Data
JCM models and registers cell populations across preprocessed flow-cytometry samples. Its demonstrations reuse three prior datasets, with manual gates, selected panels and selected benchmark samples. The implemented model restricts the general formulation. Exploratory results and nested cells do not establish prospective clinical prediction or independent replication. Nolan contributed materials, tools and writing. Source inconsistencies in timing, marker counts, tables, references and equations remain unresolved.
Read the paper at ebi.ac.ukWhat we checked
All 106 supplied XML units and 29 references were read, with no meaningful text/tail gaps. Two main figures, two tables and 216 cell fields were inspected, plus 89 native equation images in 12 viewed sheets. All 12 offered static supplements were read: seven single-frame TIFFs and five PDFs spanning 16 pages, including 180 supplementary table fields. The current publisher PDF was received through its ordinary public link and all 11 page layouts inspected. Figure 2C includes 16 markers, 28 columns and 448 colour positions. Root reviewed the full analytical packet and verified frozen files and native authors; the editor is excluded from the 13-author list. Tiny identifiers, unprinted values, historical versions and original validation remain incomplete.
Complete supplied main and static supplements read
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- Some Figure 2A i/j identifiers remain uncertain; unprinted heatmap, contour and timing coordinates remain unknown. Reading native equations does not establish their mathematical or implementation validity. Duplicate GIFs add no content credit.
- Historical scientific revisions and corrections were not compared. PMC’s repository change date is distinct from a scientific revision. Native XML states CC BY 4.0; the PDF says Creative Commons Attribution without a version.
- Maier 2007, Irish 2010 and FlowCAP datasets are reused. Three TCR donors, 28 pretherapy cases and 16 selected benchmark samples constrain generalization; the relation of three posttherapy samples to the 28 cases is unspecified. Raw data, preprocessing and software were not independently reproduced.
- Exploratory q=.058 does not meet FDR .05. Selected manually gated benchmark samples and implementation restrictions limit comparison. Timing, marker counts, rounding, suffixes, reference labels and native equation irregularities remain uncorrected.
Source limitations
- Nolan’s materials/tools and writing roles are specifically attributed; he is not credited with conception, experiments or data analysis here. ARC funding is attributed to other authors. No government approach, UAP programme, private patient collection or prospective clinical validation is established.
Cite this record
Saumyadipta Pyne, Sharon X. Lee, Kui Wang, Jonathan Irish, Pablo Tamayo, Marc-Danie Nazaire, Tarn Duong, Shu-Kay Ng, David Hafler, Ronald Levy, Garry P. Nolan, Jill Mesirov, Geoffrey J. McLachlan. Joint Modeling and Registration of Cell Populations in Cohorts of High-Dimensional Flow Cytometric Data. July 1, 2014. BioParity S7563. https://bioparity.io/sources/S7563Record data (JSON)