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Operational Qualification (OQ) Protocol

Document ID: OQ-DESEQ2-001
Version: 1.0
Date: 2026-05-24
Author: Bhavitha Kandru (kandru.b@northeastern.edu)
Status: Approved
Traces to: FRS-DESEQ2-001

1. Purpose

This OQ protocol verifies that each functional requirement defined in FRS-DESEQ2-001 is met by the implementation.

2. Prerequisites

  • IQ-DESEQ2-001 has been completed with a status of "Approved" or "Approved with deviations"
  • Test scripts in tests/ are present and executable

3. Test Cases — Data Integrity (Automated)

TC-DI-001 — Missing counts file is rejected

Field Detail
Procedure Rscript tests/test_data_integrity.R
Expected Test "TC-DI-001" reports PASS
Traces to FRS-002
Actual ____________________________________________________________
Pass/Fail _____

TC-DI-002 — Sample sheet missing required column is rejected

Field Detail
Procedure Rscript tests/test_data_integrity.R
Expected Test "TC-DI-002" reports PASS
Traces to FRS-003
Actual ____________________________________________________________
Pass/Fail _____

TC-DI-003 — Sample in sheet but not in counts is detected

Field Detail
Procedure Rscript tests/test_data_integrity.R
Expected Test "TC-DI-003" reports PASS
Traces to FRS-004
Actual ____________________________________________________________
Pass/Fail _____

TC-DI-004 — Valid inputs return correctly structured data

Field Detail
Procedure Rscript tests/test_data_integrity.R
Expected Test "TC-DI-004" reports PASS
Traces to FRS-002, FRS-003, FRS-004
Actual ____________________________________________________________
Pass/Fail _____

4. Test Cases — Reproducibility

TC-RP-001 — Two consecutive runs produce identical results

Field Detail
Procedure Rscript tests/test_reproducibility.R
Expected Test reports PASS; log2FoldChange and padj columns are bit-identical
Traces to URS-008, FRS-NF2
Actual ____________________________________________________________
Pass/Fail _____

5. Test Cases — Output Format

TC-OF-001 — Output TSV contains all required columns

Field Detail
Procedure Run analysis, then: head -1 results/deseq2_results.tsv
Expected First line contains: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj
Traces to FRS-006
Actual ____________________________________________________________
Pass/Fail _____

TC-OF-002 — Software versions log is created

Field Detail
Procedure Run analysis, then: cat results/software_versions.log
Expected Log contains R version, DESeq2 version, readr version, timestamp, user
Traces to FRS-007
Actual ____________________________________________________________
Pass/Fail _____

TC-OF-003 — Serialized RDS object is loadable

Field Detail
Procedure Rscript -e 'class(readRDS("results/dds.rds"))'
Expected Output is "DESeqDataSet"
Traces to FRS-009
Actual ____________________________________________________________
Pass/Fail _____

6. Test Cases — Data Immutability

TC-IM-001 — Input files are not modified during analysis

Field Detail
Procedure Capture SHA-256 of inputs before and after run: shasum -a 256 data/test_counts.tsv data/test_samples.csv
Expected Hash values are identical before and after
Traces to FRS-008, URS-010
Actual ____________________________________________________________
Pass/Fail _____

7. OQ Summary

Total test cases 9
Passed _____
Failed _____
OQ status □ Approved □ Approved with deviations □ Rejected
Deviations (if any) _________________________________________________

8. Approval

Role Name Date Signature
Performed by _____ _____ _____
Reviewed by _____ _____ _____
Approved by _____ _____ _____