tpmjs/packages/tools/official/multiple-testing-adjust

@tpmjs/tools-multiple-testing-adjust

Adjust p-values for multiple testing using Bonferroni, Benjamini-Hochberg (BH), or Holm methods to control family-wise error rate or false discovery rate.

Installation

npm install @tpmjs/tools-multiple-testing-adjust

Usage

import { multipleTestingAdjustTool } from '@tpmjs/tools-multiple-testing-adjust';

// Use with AI SDK
const result = await multipleTestingAdjustTool.execute({
  pValues: [0.001, 0.02, 0.03, 0.15, 0.8],
  method: 'bh', // 'bonferroni', 'bh', or 'holm'
  alpha: 0.05,
});

console.log(result);
// {
//   adjusted: [0.005, 0.05, 0.05, 0.1875, 0.8],
//   significant: [0, 1, 2],  // Indices of significant tests
//   method: 'bh',
//   alpha: 0.05,
//   metadata: {
//     totalTests: 5,
//     significantCount: 3,
//     originalSignificant: 3
//   }
// }

Parameters

• pValues (number[], required): Array of p-values to adjust (each between 0 and 1)
• method (string, optional): Adjustment method - 'bonferroni', 'bh', or 'holm' (default: 'bonferroni')
• alpha (number, optional): Significance level (default: 0.05)

Returns

{
  adjusted: number[];        // Adjusted p-values in original order
  significant: number[];     // Indices of tests that remain significant
  method: string;            // Method used
  alpha: number;             // Significance level
  metadata: {
    totalTests: number;
    significantCount: number;      // Count after adjustment
    originalSignificant: number;   // Count before adjustment
  }
}

Methods

Bonferroni

• Most conservative method
• Controls family-wise error rate (FWER)
• Multiplies each p-value by the number of tests
• Use when you need strict control over false positives

Benjamini-Hochberg (BH)

• Controls false discovery rate (FDR)
• Less conservative than Bonferroni
• Better power for large numbers of tests
• Recommended for exploratory analyses

Holm

• Step-down procedure
• Controls FWER like Bonferroni but more powerful
• Good middle ground between Bonferroni and BH
• Use when you want FWER control with better power

When to use

• When performing multiple hypothesis tests simultaneously
• To avoid inflated Type I error rates
• In genomics, neuroimaging, A/B testing with multiple variants
• Any study with multiple comparisons

Example: Comparing methods

const pValues = [0.001, 0.01, 0.02, 0.03, 0.05, 0.1];

// Bonferroni (most strict)
const bonf = await multipleTestingAdjustTool.execute({
  pValues,
  method: 'bonferroni',
});
// significant: [0] - only the smallest p-value survives

// Holm (moderate)
const holm = await multipleTestingAdjustTool.execute({
  pValues,
  method: 'holm',
});
// significant: [0, 1] - two tests survive

// BH (least strict)
const bh = await multipleTestingAdjustTool.execute({
  pValues,
  method: 'bh',
});
// significant: [0, 1, 2, 3] - four tests survive

License

MIT