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BH independent FDR
1 · Prerequisites
- Binary Operations, Monoids, Groups and Subgroups
- Construction of the Natural Numbers
- Construction of the Real Numbers via Cauchy Sequences
- Construction of the Real Numbers via Dedekind Cuts
- Cosets, Index and Lagrange's Theorem
- Countability and Uncountability
- Divisibility, Euclidean Domains, Principal Ideal Domains and Unique Factorisation
- Estimators and Randomized Procedures
- Finite Counting, Factorials and Binomial Coefficients
- Foundations of the Real Numbers for Analysis
- Ideals, Quotient Rings and the Isomorphism Theorems for Rings
- Independence Borel Cantelli and Zero One Laws
- limsup, liminf, and Subsequential Limits
- Measurable Functions and Simple Approximation
- Measures and Their Basic Properties
- Monotone Sequences, Bolzano-Weierstrass, and Cauchy Completeness
- Normal Subgroups and Quotient Groups
- Order, Zorn's Lemma, and the Axiom of Choice
- Polynomial Rings, the Division Algorithm and Roots
- Probability Spaces Random Variables and Expectation
- Product Measures and the Fubini Tonelli Theorems
- Relations, Functions, and Quotients
- Rings, Subrings, Integral Domains and Fields
- Roots, Rational Powers, and Classical Inequalities
- Sequences and Limits
- Sigma Algebras and Borel Sets
- Simple Field Extensions and the Construction of the Complex Numbers
- Statistical Experiments, Models and Identifiability
- Suprema and Infima
- Tests, Neyman–Pearson and Valid P-values
- The Lebesgue Integral and the Convergence Theorems
- The ZFC Axioms and the Basic Set Constructions
- Topological Spaces and Continuity
- Topology of ℝ
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 true-null p-values, a leave-one-out identity gives the exact FDR . 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
False discovery proportion, FDR, and FWER
Definition
Let be a finite number of hypotheses and write . Fix a probability law and a set of indices whose null hypotheses are true under . A measurable rejection rule is a measurable map , where the finite set has its discrete sigma-algebra. Set
The false discovery proportion is
and the false discovery rate is
The family-wise error rate is
Since whenever and when , the FDP is a measurable random variable in 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.
Benjamini–Hochberg step-up procedure
Definition
Input p-values and a level . Order the hypotheses by the keys , so equal p-values are ordered by their original index, and write the ordered values as . Set
Reject exactly the hypotheses at ranks . If the set in the maximum is empty, then and no hypothesis is rejected. This is a deterministic step-up rule for the supplied p-values; its FDR guarantee is a separate theorem.
Leave-one-out identity for the BH step-up rule
Statement
Let , , and let be measurable -valued functions on one measurable space. Apply the algorithm in Benjamini–Hochberg step-up procedure. For each and vector , order the remaining values as and define
When , set . Let , let be the number of rejections, and let be the indicator that hypothesis is rejected. Then is measurable with respect to the sigma-algebra generated by the other coordinates and, pointwise,
Facts & Assumptions
Given: , , measurable functions , and the step-up algorithm specified in the Statement.
Benjamini–Hochberg step-up procedure: order the p-values and let be the largest rank satisfying ; reject ranks , taking when no rank qualifies.
A measurable function between measurable spaces: a function is measurable when the preimage of every measurable codomain set is measurable.
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
For every and real , , since the th smallest value is at most exactly when at least coordinates are at most ; 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.
Each is measurable by step 1.1; its indicator and the simple function are measurable by [F2], and the finite maximum of these functions and is measurable because its sublevel sets are finite intersections. The same construction with and thresholds shows each level set of lies in the sigma-algebra generated by the remaining coordinates.
If , no is zero because then , so no value is at most . If , maximality gives and , so exactly the first ranks have values at most ; if , all values are at most . Thus the rejected indices are exactly .
Fix and write . If , then , and if there are no other values to check. When , at least full-family values meet that threshold, so . If , the qualifying rank has ; deleting leaves at least other values at most , making qualify in the definition of , a contradiction. Hence , and step 3.1 shows that is rejected.
If but is rejected, step 3.1 gives ; write . At least other values are at most , so qualifies in the definition of (with automatically qualifying when ). Thus , whence , a contradiction; therefore is not rejected.
Step 4.1 shows that implies and , while step 4.2 shows that otherwise ; substituting these two cases gives the stated pointwise identity.
Benjamini–Hochberg FDR under independence
Statement
Let be a statistical experiment, let , and fix a prespecified family of nonempty null hypotheses with valid p-value statistics . For each , put
Suppose that under every the p-values are mutually independent and that
False-null p-value laws may otherwise be arbitrary. For every , the BH rule in Benjamini–Hochberg step-up procedure satisfies
This is an FDR guarantee; no FWER bound is asserted.
Facts & Assumptions
Given: The fixed finite family and statistical experiment in the Statement, , and the stated independence and exact-uniformity conditions under each .
False discovery proportion, FDR, and FWER: for true-null index set , counts rejected true nulls, is the number rejected, and .
Benjamini–Hochberg step-up procedure: for sorted values , BH takes the largest with and rejects the first ranks.
Valid p-values: a p-value statistic is a measurable statistic into ; validity requires under every null law.
Independent random elements: random elements on one probability space are independent when their generated sigma-algebras are independent.
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.
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.
Leave-one-out identity for the BH step-up rule: for each , the leave-one-out variable is measurable with respect to the other p-values, and .
The expectation of an indicator is the probability of the event: for every event , .
Linearity, monotonicity, and the modulus bound for expectation: finite sums of integrable random variables have expectation equal to the sum of their expectations.
Expectation of a nonnegative or integrable random variable: expectation is the integral against the specified probability law.
For every fixed , the p-values are mutually independent under , and each has the exact uniform law, so on .
Proof
Fix and work on the probability space , regarding each as a random element; [F3] makes these functions measurable. For and , , so each rank-threshold event is measurable. The events are finite Boolean combinations of the rank-threshold events, so is measurable. If , maximality in [F2] gives and , so the rejected hypotheses are exactly those with . If , all values are at most ; if , no value is zero because then rank would qualify. Hence the same characterization holds in every case. The rejection events are measurable because , so the BH rule is a measurable map into the finite set . Now fix . [A1] and [F4] give independence; [F5] groups and the remaining , while [F7] makes measurable with respect to the latter group. Thus and are independent random elements, and [F6] gives their product joint law.
For put . By [A1], ; independence from step 1.1 and the product law [F6] give .
By [F7], partitioning on the finite-valued expresses as . Each event is measurable, and [F8] and [F10] give the absolute expectation of its summand as , so each summand is integrable. Then [F8], [F9], and step 2.1 give .
The measurable BH rejection rule from step 1.1 lets us apply [F1] with and . Thus and ; repeated finite linearity [F9] and step 3.1 give , since . 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
- Yoav Benjamini and Yosef Hochberg, Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing, JRSS B 57(1) (1995), §2 and §3.1
- Yoav Benjamini and Yosef Hochberg, Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing, JRSS B 57(1) (1995), §3.1
- STATS 200: Introduction to Statistical Inference, Lecture 11: Testing Multiple Hypotheses, Stanford University, PDF pp. 28–29
- Yoav Benjamini and Yosef Hochberg, Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing, JRSS B 57(1) (1995), Theorem 1 and Appendix A
- Yoav Benjamini and Daniel Yekutieli, The Control of the False Discovery Rate in Multiple Testing under Dependency, The Annals of Statistics 29(4) (2001), §5, PDF pp. 16–17
- STATS 200: Introduction to Statistical Inference, Lecture 11: Testing Multiple Hypotheses, Stanford University, PDF pp. 32–36
- STATS 200: Introduction to Statistical Inference, Lecture 11: Testing Multiple Hypotheses, Stanford University, PDF pp. 28–36