4 RNA-seq: design, results, and interpretation

4.1 Learning objective

Evaluate the scientific reasoning, reproducibility, and interpretation of a rnaseq analysis.

4.2 Case specification

Support level: Guided.

Planned scenario: A synthetic two-condition expression study with sample metadata and a batch variable.

Evaluation question: Can the supplied design support the reported expression differences and interpretation?

This is an original case design. Data and scientific conclusions have not yet been generated or validated.

4.3 Planned evidence package

See cases/rnaseq/case-specification.md. The completed package will contain a data dictionary, input data, supplied response, code, output tables, and an independently verified reference analysis.

4.4 Review priorities

Sample-to-count alignment
Biological replication and design structure
Effect sizes, uncertainty, and multiple-testing interpretation
Consistency between the results table and biological claims

4.5 Learner workflow

Read the question and inventory the supplied evidence.
Extract claims from the supplied response.
Mark each claim supported, incorrect, unsupported, or uncertain.
Run or inspect the relevant verification checks.
Update your judgment and explain any correction.
Complete the evidence log and self-assess with the rubric.

4.6 Checkpoint

Which conclusions survive verification, and which require correction or additional evidence?

4.7 Deliverable

A case review using templates/evaluation-report.qmd and templates/evidence-log.csv.

4.8 Worked explanation

To be authored after the reference workflow and expected outputs have been verified. Include valid reasoning as well as errors, and discuss defensible alternative interpretations.