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jean — Molecular Biology & Genomics

estimate_effect_size

Read-only

The effect a power calculation needs, measured from a pilot instead of guessed: two groups of one measurement in a table, standardised as Hedges' g (default), Cohen's d or Glass's Δ with its noncentral-t confidence interval (effectsize 1.0.3, reproduced), and the two-sample t design sized at the estimate and at the interval limit nearest zero. A column can be subtracted row by row first (a reference gene's Ct, giving delta-Ct). Returns the design calculate_power takes: Cohen's d for the t test, the raw difference and SD for t_raw.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
ciNothe confidence level of the interval.
groupNothe group compared. Left unset, the second group to appear.
powerNosize the design for this power; leave empty to estimate the effect only.
tableYesthe pilot: a header row, then one row per observation. Tab- or comma-separated.
valueYesthe column holding the measurement.
_filesNoThe project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
groupsNoone group label per data row, in row order, separated by commas, spaces or new lines, when the table has no group column.
pairedNothe two groups are the same subjects measured twice, paired by row order within each group. Only applies when estimator is hedges_g or cohens_d.
_subjectNoThe record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
subtractNoa column subtracted from the measurement row by row before anything else: a reference gene's Ct (giving delta-Ct), a baseline.
estimatorNoHedges' g corrects Cohen's d's small-sample bias by the exact J(df); Cohen's d is the uncorrected standardised difference; Glass's Δ standardises by the reference group's SD alone, for when the treatment changes the spread. Values: hedges_g (Hedges' g), cohens_d (Cohen's d), glass_delta (Glass's Δ).hedges_g
pooled_sdNostandardise by the pooled SD (Student). Off averages the two variances, with Welch's df. Only applies when estimator is hedges_g or cohens_d.
referenceNothe group it is compared against (the control). Left unset, the first group to appear.
sig_levelNoα for the sizing. Advanced.
alternativeNoa two-sided interval, or one bounded on one side. Values: two.sided (Two-sided), less (Less (upper bound only)), greater (Greater (lower bound only)). Advanced.two.sided
group_columnNothe column naming each row's group. Or give `groups`.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
designYeswhat calculate_power takes: the t test's d (`effect`), and the raw `difference` and `sd` for t_raw
groupsYesevery group in the table: n, mean and SD of the measurement
sizingYespwr.t.test's sample size at the estimate and at the limit nearest zero, when power was given
estimateYesthe standardised effect
intervalYesthe confidence interval: level, low, high

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.1/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so the safety profile is covered. The description adds real behavioral context beyond that: the default estimator, that a column can be subtracted row-by-row before analysis (delta-Ct), that the design is sized both at the estimate and at the interval limit nearest zero, and what the output feeds into.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Front-loaded with the core purpose ('The effect a power calculation needs...'), and the second sentence cleanly covers the return/handoff. The prose is dense and jargon-heavy with a provenance aside ('effectsize 1.0.3, reproduced'), but each clause carries substantive information rather than filler.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists, so return values need not be spelled out, and the description still notes what the result is used for. For a 16-parameter statistical tool with full schema coverage, the description gives enough to call it correctly; the main gap is the absence of explicit alternatives/preconditions.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the schema already documents all 16 parameters including the estimator choices, paired/pooled_sd constraints and group/reference defaults. The description echoes the estimator default and the subtract-for-delta-Ct behavior but adds little parameter syntax or format detail beyond the schema, so the baseline 3 is appropriate.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb (estimate/measure) and resource (effect size from pilot data) and immediately frames it against the alternative ('measured from a pilot instead of guessed'). It also distinguishes itself from the sibling calculate_power by noting it 'Returns the `design` calculate_power takes', so an agent can place it in the workflow without opening either schema.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Clear context: use this when you have pilot measurements and need the effect size a power calculation requires, and it explicitly hands off to calculate_power. It stops short of naming when NOT to use it or listing other alternatives (e.g. calculate_rnaseq_power), so no explicit exclusions.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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