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Why Trust LFQ

This page is about the current flagship lfq surface.

What you can trust here is the repo's honesty around missingness, QC, and bounded cohort interpretation across two public LFQ packages plus one published cross-package report. The repository earns a bounded outsider-auditable LFQ claim, not broad cohort-transfer or decision-grade quant authority.

This page is one of the clearest examples of the repository being stronger and more honest at the same time. LFQ now has a fuller outsider-readable packet than earlier docs admitted, but the release sentence still narrows because the package surfaces show the narrowing pressure directly.

Open First

  • benchmark:lfq_cohort_repeatability
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package/package_manifest.json
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package/evidence/study_scale_ms1_features.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package/evidence/study_scale.design.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package/quality_sheet.json
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_sparse_contrast_review_package/package_manifest.json
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_sparse_contrast_review_package/cross_package_generalization.json

Current Trust Earned

  • outsider_review:lfq is complete enough to count as an outsider-auditable flagship family.
  • benchmark evidence tier is external_reproduction_package.
  • public claim support is advisory.
  • the runtime package is now lfq-cohort-review-corpus.
  • the companion family-transfer report is currently highly_stable at 0.84, but effect-direction confidence weakens on the sparse contrast package.
  • the recommendation posture is recommend_with_downgrade.
  • the lab posture is exploratory_only.
  • decision-grade wording remains blocked because the shared consequence chain still ends at exploratory-only follow-up and can collapse under higher assay burden.

Best Cross-Surface Audit

What The Reader Is Really Auditing

  • whether missingness, normalization, and replicate pressure are explicit enough to survive skeptical review
  • whether the runtime lane preserves reviewability across cohort-scale normalization and differential outputs
  • whether the sparse companion package weakens the same conclusions the primary package seems to support

Why This Packet Is Scientifically Real

  • LFQ now exposes a real outsider-readable chain through cohort design, missingness, normalization, runtime review, recommendation posture, and lab burden
  • the sparse-contrast companion package prevents one neat cohort packet from standing in for broader transfer confidence
  • the product value is honest review-grade abundance interpretation, not decision-grade quantification theater

Exact Claims

  • LFQ review preserves study-design semantics, missingness visibility, and repeatable rollup behavior across the bundled cohort package
  • LFQ benchmark outputs can support review-grade abundance interpretation when QC and replicate caveats remain explicit

Why This Surface Is Stronger Now

  • LFQ now publishes a fuller outsider-readable packet than the older docs made visible
  • the sparse-contrast companion package forces effect-direction weakness into the public story instead of letting the primary cohort package dominate the wording alone
  • runtime, recommendation, and consequence pages now make the bounded review-grade sentence easier to inspect as one chain

What You Can Trust Right Now

  • the repository will not hide missingness or QC weakness behind smooth summary prose
  • the repo keeps comparator and generalization limits visible instead of flattening the current package into universal cohort truth
  • the tracked public package keeps cohort design, feature evidence, and package lifecycle visible instead of implied
  • the runtime bundle now shows normalization, missingness, differential, and review outputs as one checked flagship run family
  • the companion sparse-contrast package publishes a second family-transfer check at packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_sparse_contrast_review_package/cross_package_generalization.json

Why The Released Sentence Still Narrows

  • LFQ is outsider-auditable in the packet sense, but its released sentence remains review-grade bounded
  • missingness and normalization pressure stay visible in the public acceptance surfaces
  • sparse-cohort transfer still weakens effect-direction confidence

Honest Reader Outcome

  • a reviewer should leave seeing LFQ as a real, inspectable family rather than a thin placeholder
  • the same reviewer should still refuse broader cohort-transfer or decision-grade quant language

What You Should Not Trust Yet

  • comparator drift or missing external execution parity still materially limits this public workflow claim
  • effect-direction confidence weakens on the sparse companion cohort
  • broad generalization beyond the two current cohort packages is not earned

Consequence Boundary

  • open Workflow Consequence Maps before widening LFQ language beyond a bounded recommendation
  • open What Changed The Recommendation before claiming that one extra cohort or follow-up loop materially changed the call
  • open Workflow Refusal Handbook when the next honest move may still be stop, rerun, narrow, or refuse
  • one doubled assay burden or one weak observed outcome still demotes the public sentence faster than this page alone might suggest

Evidence Grounding