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BH independent FDR

1 · Prerequisites

2 · Summary

This page defines false discovery proportion, false discovery rate, and family-wise error rate for a fixed finite testing family, then specifies the Benjamini–Hochberg step-up rule. Under mutual independence of all p-values and exact Uniform(0,1) true-null p-values, a leave-one-out identity gives the exact FDR (m0/m)q. False-null p-value laws may be arbitrary subject to the stated independence. The result concerns FDR, not FWER; dependent tests and discrete superuniform true-null extensions require separate arguments.

3 · Logical flowchart

4 · Definitions, theorems and proofs

DefinitionDefinition: Literature-sourcedProof: Not applicablejudge pass (gpt-6-luna)Open item page →

False discovery proportion, FDR, and FWER

Definition

Let m≥1 be a finite number of hypotheses and write [m]={1,…,m}. Fix a probability law P and a set I0⊆[m] of indices whose null hypotheses are true under P. A measurable rejection rule is a measurable map R:Ω→2[m], where the finite set 2[m] has its discrete sigma-algebra. Set

R=∣R∣,V=∣R∩I0∣.

The false discovery proportion is

FDP⁡:=VR∨1,R∨1:=max⁡(R,1),

and the false discovery rate is

FDR⁡:=EP ⁣[VR∨1].

The family-wise error rate is

FWER⁡:=P(V≥1).

Since V≤R whenever R>0 and V=0 when R=0, the FDP is a measurable random variable in [0,1] and its expectation is finite. These definitions use the fixed true-null set for the specified law; they do not assert that FDR and FWER are equal except in the global-null case.

AlgorithmAlgorithm: Literature-sourcedProof: Not applicablejudge pass (gpt-6-luna)Open item page →

Benjamini–Hochberg step-up procedure

Definition

Input m≥1 p-values p1,…,pm∈[0,1] and a level q∈(0,1). Order the hypotheses by the keys (pi,i), so equal p-values are ordered by their original index, and write the ordered values as p(1)≤⋯≤p(m). Set

R:=max⁡({k∈{1,…,m}:p(k)≤kq/m}∪{0}).

Reject exactly the hypotheses at ranks 1,…,R. If the set in the maximum is empty, then R=0 and no hypothesis is rejected. This is a deterministic step-up rule for the supplied p-values; its FDR guarantee is a separate theorem.

LemmaStatement: AI-adaptedProof: AI-adaptedprecheck passjudge pass (gpt-6-luna)Open item page →

Leave-one-out identity for the BH step-up rule

Statement

Let m≥1, q∈(0,1), and let P1,…,Pm be measurable [0,1]-valued functions on one measurable space. Apply the algorithm in Benjamini–Hochberg step-up procedure. For each i∈{1,…,m} and vector x−i∈[0,1]m−1, order the remaining values as x−i,(1)≤⋯≤x−i,(m−1) and define

si(x−i):=max⁡({0}∪{k∈{1,…,m−1}:x−i,(k)≤(k+1)q/m}).

When m=1, set si=0. Let Si=si(P−i), let R be the number of rejections, and let Ii be the indicator that hypothesis i is rejected. Then Si is measurable with respect to the sigma-algebra generated by the other coordinates and, pointwise,

IiR∨1=1{Pi≤(Si+1)q/m}Si+1.

Facts & Assumptions

Given: m≥1, q∈(0,1), measurable functions Pi:Ω→[0,1], and the step-up algorithm specified in the Statement.

[F1]

Benjamini–Hochberg step-up procedure: order the p-values and let R be the largest rank k satisfying p(k)≤kq/m; reject ranks 1,…,R, taking R=0 when no rank qualifies.

[F2]

A measurable function between measurable spaces: a function is measurable when the preimage of every measurable codomain set is measurable.

[F3]

The Borel sigma-algebra of a topological space: the Borel sigma-algebra is generated by the open sets; in particular, closed half-lines and their finite intersections and unions are Borel.

Proof

1.1givenF2F3construct

For every k∈{1,…,m} and real a, {P(k)≤a}=⋃J⊆{1,…,m}, ∣J∣=k⋂j∈J{Pj≤a}, since the kth smallest value is at most a exactly when at least k coordinates are at most a; the half-line is Borel by [F3], so [F2] makes this finite union of measurable intersections measurable, and the same formula works after deleting any coordinate.

2.1F2step 1.1

Each Ak={P(k)≤kq/m} is measurable by step 1.1; its indicator and the simple function k1Ak are measurable by [F2], and the finite maximum of these functions and 0 is measurable because its sublevel sets are finite intersections. The same construction with P−i,(k) and thresholds (k+1)q/m shows each level set of Si lies in the sigma-algebra generated by the remaining coordinates.

3.1F1step 2.1algebra

If R=0, no Pi is zero because then P(1)=0≤q/m, so no value is at most Rq/m=0. If 0<R<m, maximality gives P(R)≤Rq/m and P(R+1)>(R+1)q/m>Rq/m, so exactly the first R ranks have values at most Rq/m; if R=m, all values are at most P(m)≤q=mq/m. Thus the rejected indices are exactly {i:Pi≤Rq/m}.

4.1givenF1step 3.1choose

Fix i and write s=Si. If s≥1, then P−i,(s)≤(s+1)q/m, and if s=0 there are no other values to check. When Pi≤(s+1)q/m, at least s+1 full-family values meet that threshold, so R≥s+1. If R≥s+2, the qualifying rank R has P(R)≤Rq/m; deleting Pi leaves at least R−1 other values at most Rq/m, making R−1≥s+1 qualify in the definition of Si, a contradiction. Hence R=s+1, and step 3.1 shows that i is rejected.

4.2F1step 3.1algebra

If Pi>(s+1)q/m but i is rejected, step 3.1 gives Pi≤Rq/m; write r=R≥1. At least r−1 other values are at most rq/m, so r−1 qualifies in the definition of Si (with 0 automatically qualifying when r=1). Thus r−1≤s, whence Pi≤rq/m≤(s+1)q/m, a contradiction; therefore i is not rejected.

5.1step 4.1step 4.2algebra∎

Step 4.1 shows that Pi≤(s+1)q/m implies Ii=1 and R=s+1, while step 4.2 shows that otherwise Ii=0; substituting these two cases gives the stated pointwise identity.

TheoremStatement: Literature-sourcedProof: AI-adaptedprecheck passjudge pass (gpt-6-luna)Open item page →

Benjamini–Hochberg FDR under independence

Statement

Let E=((X,A),Θ,(Pθ)θ∈Θ) be a statistical experiment, let m≥1, and fix a prespecified family of nonempty null hypotheses H01,…,H0m⊆Θ with valid p-value statistics pi:X→[0,1]. For each θ, put

I0(θ)={i:θ∈H0i},m0(θ)=∣I0(θ)∣.

Suppose that under every Pθ the m p-values are mutually independent and that

Pθ({x∈X:pi(x)≤u})=u(i∈I0(θ), 0≤u≤1).

False-null p-value laws may otherwise be arbitrary. For every q∈(0,1), the BH rule in Benjamini–Hochberg step-up procedure satisfies

FDR⁡θ=m0(θ)mq≤q.

This is an FDR guarantee; no FWER bound is asserted.

Facts & Assumptions

Given: The fixed finite family and statistical experiment in the Statement, q∈(0,1), and the stated independence and exact-uniformity conditions under each Pθ.

[F1]

False discovery proportion, FDR, and FWER: for true-null index set I0, V counts rejected true nulls, R is the number rejected, and FDR⁡=E[V/(R∨1)].

[F2]

Benjamini–Hochberg step-up procedure: for sorted values p(k), BH takes the largest R with p(R)≤Rq/m and rejects the first R ranks.

[F3]

Valid p-values: a p-value statistic is a measurable statistic into [0,1]; validity requires Pθ(pi≤u)≤u under every null law.

[F4]

Independent random elements: random elements on one probability space are independent when their generated sigma-algebras are independent.

[F5]

Disjoint groups of an independent sigma-algebra family remain independent: disjoint groups of an independent family of sigma-algebras remain independent after taking the sigma-algebras they generate.

[F6]

Independent random elements have product joint law: a finite independent family of random elements has joint law equal to the finite product of its marginal laws.

[F7]

Leave-one-out identity for the BH step-up rule: for each i, the leave-one-out variable Si is measurable with respect to the other p-values, and Ii/(R∨1)=1{pi≤(Si+1)q/m}/(Si+1).

[F8]

The expectation of an indicator is the probability of the event: for every event A, E[1A]=P(A).

[F9]

Linearity, monotonicity, and the modulus bound for expectation: finite sums of integrable random variables have expectation equal to the sum of their expectations.

[F10]

Expectation of a nonnegative or integrable random variable: expectation is the integral against the specified probability law.

[A1]

For every fixed θ, the p-values are mutually independent under Pθ, and each i∈I0(θ) has the exact uniform law, so Pθ({x∈X:pi(x)≤u})=u on [0,1].

Proof

1.1givenA1F2F3F4F5F6F7choose

Fix θ and work on the probability space (X,A,Pθ), regarding each Pi:=pi as a random element; [F3] makes these functions measurable. For k∈{1,…,m} and a∈R, {P(k)≤a}=⋃J⊆[m], ∣J∣=k⋂j∈J{Pj≤a}, so each rank-threshold event is measurable. The events {R=r} are finite Boolean combinations of the rank-threshold events, so R is measurable. If 0<R<m, maximality in [F2] gives P(R)≤Rq/m and P(R+1)>(R+1)q/m>Rq/m, so the rejected hypotheses are exactly those with Pi≤Rq/m. If R=m, all values are at most q=Rq/m; if R=0, no value is zero because then rank 1 would qualify. Hence the same characterization holds in every case. The rejection events are measurable because {Pi≤Rq/m}=⋃r=0m({R=r}∩{Pi≤rq/m}), so the BH rule is a measurable map into the finite set 2[m]. Now fix i∈I0(θ). [A1] and [F4] give independence; [F5] groups Pi and the remaining Pj, while [F7] makes Si measurable with respect to the latter group. Thus Pi and Si are independent random elements, and [F6] gives their product joint law.

2.1A1F6step 1.1algebra

For r∈{0,…,m−1} put tr=(r+1)q/m≤q<1. By [A1], Pθ(Pi≤tr)=tr; independence from step 1.1 and the product law [F6] give Pθ(Pi≤tr, Si=r)=trPθ(Si=r).

3.1F7F8F9F10step 2.1algebra

By [F7], partitioning on the finite-valued Si expresses Ii/(R∨1) as ∑r=0m−11{Pi≤tr,Si=r}/(r+1). Each event is measurable, and [F8] and [F10] give the absolute expectation of its summand as Pθ(Pi≤tr,Si=r)/(r+1)≤1, so each summand is integrable. Then [F8], [F9], and step 2.1 give Eθ[Ii/(R∨1)]=∑r=0m−1trPθ(Si=r)/(r+1)=(q/m)∑r=0m−1Pθ(Si=r)=q/m.

4.1F1F9step 1.1step 3.1algebra∎

The measurable BH rejection rule from step 1.1 lets us apply [F1] with P=Pθ and I0=I0(θ). Thus V=∑i∈I0(θ)Ii and FDR⁡θ=Eθ[V/(R∨1)]; repeated finite linearity [F9] and step 3.1 give FDR⁡θ=∑i∈I0(θ)q/m=(m0(θ)/m)q≤q, since m0(θ)≤m. This is the FDR defined in [F1], not an FWER conclusion.

Remarks

No choice axiom is used: the family is finite, each leave-one-out index is fixed in the proof, and the product-law supplier is applied only to finite families.

5 · Examples, counterexamples and false statements

None yet.

Sources