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Analysisstrong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.

[CORRECTED cycle 117 - the columns were not scaled] Correcting yesterday's correction: share(s) = absolute(s)/G is an exact identity, so a within-sample share reproduces the true SHAPE faithfully and misstates only the LEVEL - but that is the worse failure, because 34 of 66 strata lost up to 68% of their signal while reading as gains of up to +440%

also called the share identity · above 1 means lost less than average · 34 of 66 strata flip sign · the shape is real, the level is not

Yesterday this project concluded that its proportion-based method invents a false pattern out of nothing. That was wrong, and the arithmetic shows why: the pattern the method reports is exactly the true pattern, just rescaled. The genuine problem is different and more dangerous. A proportion only ever says how one region did compared with the average of everything. When everything is falling, a region that fell by half can still look like it doubled. In this dataset that happened to more than half of the regions examined.

The same thing, for a scientist

**Statement.** Cycle 109 graded this project's stratified-share statistic against a known answer and concluded the share *"renders a pure global collapse as a monotone gradient"* that is *"an artefact of renormalisation"*. **That is wrong**, and one line of arithmetic shows it: > **`share(s) = absolute(s) / G`**, where `G` is the global absolute ratio. **Verified to a maximum deviation of 0.00204 across all 66 strata, two cell lines and three contrasts.** A share divides every stratum by the same constant, so **it cannot create, destroy or reorder a gradient. The shape it reports is the true shape.** **Three claims in cycle 109 are retracted.** It was not *"a pure global collapse with no redistribution"* — the absolute profile spans **0.056 to 1.662, a 30-fold range**. Not *"every stratum lost signal or held"* — **D9 gained 9%, D10 gained 66%**. And the gradient is **not an artefact**. **The real failure is the level, and it is worse than the one I claimed.** A share is a statement **relative to the genome-wide average**. It never says whether a stratum gained or lost. When `G` is far from 1, those two readings separate completely: | line / contrast | G | strata that LOST but read as GAIN | worst case | |---|---:|---:|---| | RS4;11 EPZ d9 | 0.171 | **5 of 11** | D8 lost 7%, reads **+440%** | | RS4;11 comp.10 d9 | 0.223 | **6 of 11** | lost 61%, reads +328% | | MOLM13 EPZ d9 | 0.235 | **8 of 11** | lost 68%, reads +294% | | MOLM13 comp.10 d9 | 0.367 | **8 of 11** | lost 61%, reads +149% | | RS4;11 EPZ d3 | 0.765 | 4 of 11 | lost 18%, reads +27% | | MOLM13 EPZ d3 | 0.803 | 3 of 11 | lost 17%, reads +16% | **34 of 66 strata — 52% — lost signal while reading as a gain.** The hazard scales with `|1 − G|`: at the realistic d3 effect sizes (`G` ≈ 0.77–0.80) a third of strata still flip sign, but the apparent gains shrink to +16–27%. **And the consequence for cycle 103 reverses.** Because the shapes are identical, its monotone profile **is** a faithful report that the sparse strata fared better than the peaks. **Its shape claim stands.** What it — and every share-based beat here — cannot support is the step from *above 1* to *gained signal*. **PRIOR ART, AND IT IS OLDER AND DEEPER.** `concept-q124-a-within-sample-share-in-a-top-bin-set-is-anti-correlated-with-library-complexity` established that this instrument is confounded with **ChIP enrichment** — Spearman **−1.000** against non-zero bin count over four timepoints, with an enrichment-only null spanning the observed range — and that **no within-sample fix exists**. It is also why the corpus already says *"redistribution"* rather than *"loss"*. **This entry is complementary, not prior**: Q124 is about the ratio being confounded, this is about how to read it given a known `G`. A screen for entries misusing the distinction returned **70 of 117** — keyword co-occurrence, not a fault list — because the discipline was already in place. --- # ⛔ CORRECTED IN CYCLE 117 — THE DATA WAS NOT WHAT THIS ENTRY SAYS IT WAS **Two independent defects, both verified by the coordinator against the files on disk.** **1. The deposited columns are NOT spike-in scaled.** This entry asserted they were, citing the column sums. **All 1,040,292 values in both files lie exactly on a 0.04 grid (integer/25)** — only **18** exceptions, every one the `MT-TT` chrM tRNA whose window runs off the chromosome. A scale factor such as 1/9.91 would destroy that grid. **`+_dm6_spike-in` in the filename means the counts are supplied *alongside* the signal, not applied to it.** This entry's own `U3` said *"if the deposited columns were not spike-in scaled, the absolute arm is not absolute and the whole comparison collapses"* — **`U3` fired and was not noticed**, because the check used was the column sums, and a DOT1L inhibitor collapsing H3K79me2 lowers the raw sums exactly as a scaling would. **2. The RS4;11 file is two-thirds MOLM13.** **38,580 of 57,794 data rows are byte-identical to the MOLM13 file in all nine signal columns**, in a contiguous block from row 19,217 to the end. Only 19,214 rows can be RS4;11. This is a defect in the deposit as served today, not in the local copy. **What survives:** the arithmetic. `share(s) = absolute(s)/G` is an identity and the shape-versus-level distinction is unaffected. **What does not:** every statement in this entry that called the deposited values absolute, and every RS4;11-specific number. See `ana-q138-*` for the corrected absolute-scale analysis, which applies `K = dm6(DMSO)/dm6(treated)` and restricts to the 19,214 genuine rows. **And this entry's own headline correction was itself wrong in one particular.** It stated that **"D9 gained 9% and D10 gained 66%"** in absolute terms. With the spike-in factor actually applied, **D10 lost 76.5%** — nothing gained anywhere. The *shape* finding stands; the level claim that replaced cycle 109's level claim was false for the same reason cycle 109's was.

Go deeper
Why yesterday's version was wrong, and what produced the error

Cycle 109 saw the share profile rise from 0.32 at TOP to 9.70 at D10 and read it as a manufactured pattern. It never checked the absolute profile's shape, which rises from 0.056 to 1.662 over the same strata — the same 30-fold rise. Both profiles say the identical thing about ordering; only the level differs.

The error was reaching for the most alarming available reading and not testing it against the simplest possible model. share = absolute/G is one line, derivable without any data, and it falsifies the headline immediately. The pre-registration did not help: W1, W2 and the post-hoc W3 were all about how badly the statistic performs, and none of them asked in what respect.

A sibling result is unaffected and should not be swept up in this. Self-stratifying two identical libraries really does manufacture a monotone gradient of span 0.331 out of nothing — that one is a genuine artefact, established independently, and it is not what renormalisation does.

The rule that replaces the wrong one

Wrong rule (cycle 109): a rising share gradient into the sparse deciles is the signature of a global decrease.

Correct rule: a share ratio is a comparison with the genome-wide average. Its shape is trustworthy; its position relative to 1 is not. A stratum reading above 1 lost less than average — which, when the average collapsed, can still mean it lost most of its signal.

Operationally: any share-based claim of the form "X increased at stratum s" is unsupported without an estimate of G. Claims of the form "s fared better than t" are fine. Every stratified result in cycles 102–107 should be read with that distinction applied, and the ones that only ever claimed relative ordering are untouched.

Facts and figures
questionin what respect does a within-sample share mislead - shape or level?
correctsana-a-share-renders-a-global-collapse-as-a-rising-gradient-into-the-bulk
the identityshare(s) = absolute(s) / G
max deviation verified0.00204
strata checked66
what actually happenedthe absolute profile itself spans 0.056 to 1.662; D9 and D10 genuinely gained; the gradient is real
strata that lost but read as gain34
of66
PCT52
worst casea stratum that lost 7% of its signal reads as +440%
largest true loss reading as gain68%, reading +294%
hazard scales with|1 - G|; at G ~ 0.77-0.80 the flip rate is 3-4 of 11 and apparent gains are +16-27%
correct rulea share ratio is a comparison with the genome-wide average - its SHAPE is trustworthy, its position relative to 1 is not. Above 1 means 'lost less than average', not 'gained'.
effect on cycle 103its shape claim STANDS; its redistribution reading does not, because that is an absolute-level claim
absence classmeasured-not-curated
bite backThis entry tells readers that share-based SHAPE claims are safe. If G varies across the strata being compared - which happens whenever two samples differ in more than a single global factor - even the shape is not preserved, and this entry will have licensed the class of claim it was written to protect.
retracted claims
[
  "a pure global collapse with no redistribution whatsoever",
  "every stratum lost signal or held",
  "the gradient is an artefact of renormalisation"
]
THE AUDIT WAS RUN AND IS UNINFORMATIVE
{
  "what_i_did": "screened all committed entries at HEAD for share language co-occurring with absolute-gain language in the same sentence",
  "result": "70 of 117 share-using entries flagged - a keyword co-occurrence, not a fault list",
  "why_it_is_uninformative": "the corpus already enforces the distinction deliberately. concept-q124-a-within-sample-share-in-a-top-bin-set-is-anti-correlated-with-library-complexity states it explicitly: 'the reason every measurement entry in this beat says redistribution rather than loss'. The hits are overwhelmingly entries using relative language correctly, plus this entry itself, which is ABOUT the distinction.",
  "the_lesson": "a gap list cannot see what was decided - screened before checking whether the corpus had already adjudicated"
}
PRIOR ART IN THE CORPUS
{
  "entry": "concept-q124-a-within-sample-share-in-a-top-bin-set-is-anti-correlated-with-library-complexity",
  "what_it_established_first": "the share ratio is confounded with CHIP ENRICHMENT, not just with an unknown scale factor: Spearman(V, non-zero bin count) = -1.000 over four timepoints, and a null built from enrichment alone spans the observed range. Three mitigations were tried and each has a limit; there is no within-sample fix.",
  "how_this_entry_differs": "Q124 is about the ratio being CONFOUNDED. This entry is about how the ratio should be READ given a known global change: share = absolute/G, so 'above 1' means 'lost less than average'. Complementary, and Q124 is the deeper and earlier result.",
  "priority": "Q124, by many cycles"
}
CORRECTED CYCLE 117
{
  "defect_1": "the deposited columns are NOT spike-in scaled - all values on a 0.04 grid, 18 exceptions, all MT-TT",
  "defect_2": "38,580 of 57,794 rows in the RS4;11 file are byte-identical to MOLM13, contiguous from row 19,217",
  "U3_fired_unnoticed": "this entry pre-registered exactly this failure and checked column sums instead of the grid",
  "what_survives": "the share = absolute/G identity and the shape-versus-level distinction",
  "see": "the Q138 absolute-scale beat"
}
Still open
  1. Does the identity survive when G is not a single constant? It holds because a share divides every stratum by one number. Two samples differing in more than a global factor break that, and nothing here tests it.
  2. Estimate G for the contrasts in cycles 102-107. Without it, every claim of the form 'X increased at stratum s' in those beats is unsupported - and with it, most could be repaired rather than retracted.
  3. Re-read cycle 103's sentence specifically. Its shape survives; its 'flattens out of the peaks into the bulk' phrasing is an absolute-level claim and needs either a G estimate or a rewrite.
  4. Reconcile with Q124 properly. It shows the share is confounded with ChIP enrichment and that no within-sample fix exists; this entry shows how to read a share given G. Whether a spike-in-derived G repairs the enrichment confound, or is defeated by it, is unaddressed by both and is the question that matters.
Every source behind this entry (1)
  1. E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis

    Across GSE149183's two spike-in-scaled cell lines and three contrasts, 66 strata in total, the relation share(s) = absolute(s)/G holds with a maximum deviation of 0.00204, where G is the global absolute ratio for that contrast. In RS4;11 EPZ5676 d9, G = 0.1713 and the absolute stratum ratios run 0.0556 at TOP to 1.6616 at D10 while the share ratios run 0.3244 to 9.6979 - the same 30-fold rise. D9 (1.0942) and D10 (1.6616) gained signal in absolute terms. Counting strata that lost signal (absolute < 1) yet read as a gain (share > 1): 5, 6, 4, 8, 8 and 3 across the six contrasts, 34 of 66 in total, with the largest apparent gain +440% for a stratum that lost 7% and the largest true loss 68% for a stratum reading +294%.

    What this evidence cannot show

    THE IDENTITY IS ARITHMETIC AND NEEDED NO DATA - verifying it numerically checks the implementation, not the mathematics, and the interesting content is entirely in the COUNT of strata that flip sign, which is dataset-specific. The 52% figure depends on how far G sits from 1 and therefore on a drug class chosen because its effect is extreme; at the d3 contrasts, which are the closest thing here to a realistic effect size, the flip rate is 3-4 of 11 and the apparent gains are small. The assay is TSS-averaged sitepro over 57,794 genes, not the binned genome of cycles 102-107, and the mark and drug class both differ. Nothing here establishes G for any analysis in this project, so it identifies which claims are exposed without repairing any of them.

    Evidence that argues against this (3)
    • Correcting a one-day-old entry of my own may be giving that entry more weight than it earned. Its conclusion - that share-based stratified claims are unsafe when the global change is unknown - survives this correction intact; only the mechanism and the shape claim were wrong. A reader who took away the practical warning and not the explanation lost nothing, and two entries now exist where one careful one would have done.
    • The sign-flip count is the headline and it is partly definitional. 'Lost signal but reads as a gain' is guaranteed for any stratum whose absolute ratio lies between G and 1, so the count is essentially a measure of how many strata fall in that window - which widens automatically as G falls. Reporting 34 of 66 sounds like an empirical discovery and is closer to a restatement of where G sits.
    • This does not rescue cycle 103 so much as relocate the question. Its shape claim survives, but its interpretation - that the fusion's share flattens OUT of the peaks INTO the bulk - is a statement about where signal went, which is exactly the absolute-level claim a share cannot make. The correction moves the problem from 'the gradient is fake' to 'the gradient is real but cannot bear a redistribution reading', and that is still fatal to the sentence as written.
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