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fisher() returns a chi-square density on the wrong degrees of freedom, inverting the p-value #30
Description
fisher() in methods/multilist.rs does not return a p-value. Two independent defects
combine so that the result is not merely inaccurate — it inverts, reporting the least
significant inputs as the most significant.
pub fn fisher(vals: &Vec<f64>) -> f64 {
let k = vals.len();
let pt = -2.0 * vals.iter().map(|x| x.ln()).sum::<f64>();
let dist = statrs::distribution::ChiSquared::new(2_f64.powi(k as i32 - 1)).unwrap();
dist.pdf(pt)
}The statistic pt = -2 Σ ln(pᵢ) is correct. What follows is not.
1. .pdf() where an upper-tail probability is needed. Fisher's method wants
P(χ² ≥ pt), the survival function. A density is not a probability. For df > 2 the
chi-square density is zero at 0, rises to a mode, then decays — so it is small at both
ends. pt approaches 0 when every pᵢ approaches 1, which is the least significant
possible input, and that is exactly where the density is smallest.
2. 2^(k-1) degrees of freedom where 2k is needed. Exponential instead of linear:
k=3 gives 4 instead of 6, k=5 gives 16 instead of 10. Correct only at k=4, by coincidence.
Measured
| input | current | correct |
|---|---|---|
[0.999, 0.999, 0.999] |
0.0015 | 1.0 |
[0.9, 0.9, 0.9] |
0.115 | 0.996 |
[0.5, 0.5, 0.5] |
0.130 | 0.655 |
[0.05, 0.05, 0.05] |
0.00056 | 0.0063 |
[0.999] × 5 |
7.7e-21 | 1.0 |
Three p-values of 0.999 combine to 0.0015; five combine to 7.7e-21.
Reach
fisher() is pub, and MetaAnalysisMethod::Fisher is a public variant selected in
multilist_gsea (multilist.rs:96) and multilist_ora (multilist.rs:165). Any consumer of
webgestalt_lib choosing Fisher gets these values with no warning.
WebGestaltR is not currently affected. multiOraEnrichment.R:80 does pass "fisher",
so this runs on every multi-omics ORA analysis, but the R layer then discards the result and
recomputes the meta-p with poolr::stouffer (multiOraEnrichment.R:131, and
multiswGsea.R:178 for GSEA). The wrong value is computed and thrown away. That makes this
latent rather than live — and a hazard, since anyone removing the apparently redundant R
computation in favour of the Rust one would ship inverted p-values silently.
Suggested fix
pub fn fisher(vals: &Vec<f64>) -> f64 {
let k = vals.len();
let pt = -2.0 * vals.iter().map(|x| x.ln()).sum::<f64>();
let dist = statrs::distribution::ChiSquared::new(2.0 * k as f64).unwrap();
dist.sf(pt) // or 1.0 - dist.cdf(pt) if `sf` is unavailable in this statrs version
}sf is preferable to 1 - cdf — the latter loses precision in the far tail, which is where
combined p-values live.
Worth adding a doctest alongside the existing stouffer ones: combining [0.5, 0.5] should
give 0.5966 (χ² = 2.7726 on 4 df), and combining values near 1 should give a result near 1,
which is the property currently violated.
Activity
iblacksand commentedon Aug 10, 2026
As far as I am aware
fisher()is not used by any live code.webgestaltpyuses thestouffermethod for FDR correction.This is still worth correcting or removing the method completely, but this shouldn't have corrupted any existing analysis. This was sort of abandoned in favor of
stoufferzhiaos commentedon Aug 10, 2026
Thanks John — that matches what I found: the R package asks Rust for
"fisher"and then overwrites the result withpoolr::stouffer, so nothing user-facing was affected. I'll go with removing the method rather than fixing it, and reference this issue in the commit.Unrelated ask while you're here: could you add me as an owner on the two crates? I've taken over maintenance — I'm the CRAN maintainer for WebGestaltR now, and the GSEA seed fix (#31) means
webgestalt_libwill need a 0.4.0 publish, which I can't do. You're currently the sole owner of both:iblacksand commentedon Aug 11, 2026
I added you as an owner to the crate. However, I usually publish through a github release. If you create a release (or I can), then it should publish from the GitHub instance. I think this is typically preferred to show that the code from the github is what is in the published crate.
This also goes for
webgestaltpy.zhiaos commentedon Aug 11, 2026
Thanks — accepted both invites, and
cargo owner --listshows us both now. Understood on publishing via a GitHub release rather thancargo publish; I'll follow that.Closing this:
fisher(), theMetaAnalysisMethod::Fishervariant and its two match arms are removed in #36, and WebGestaltR stopped naming the method in bzhanglab/WebGestaltR#74. Nothing user-facing changed, as you said — the R layer was already discarding the Rust meta-p and recomputing withpoolr::stouffer.