bio-differential-expression-batch-correction SKILL.md skillA
bio-differential-expression-batch-correction from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-differential-expression-batch-correction@git:20261018.db2b2b5Pins git:20261018.db2b2b5 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
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skills/batch-correction--bioskills--95fa323889/SKILL.md- Versions recorded
- 1
- Latest version
- git:20261018.db2b2b5, committed Oct 18, 2026
- Size
- 22,646 bytes
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- 15
- License
- a license file GitHub does not identify
Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for negative-control-gene-anchored unwanted variation, and limma::removeBatchEffect for plotting only. Encodes the Nygaard 2016 cardinal sin against testing on a batch-corrected matrix, the choice between SVA/RUVg/RUVs/RUVr, the confounding non-identifiability problem, the single-cell boundary (Harmony/MNN are NOT for bulk)…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility
Reference examples tested with: sva 3.50+ (includes ComBat + ComBat_seq), DESeq2 1.42+, edgeR 4.0+, limma 3.58+, RUVSeq 1.36+, ggplot2 3.5+, harmony 1.2+ (single-cell context only)
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# Batch Effect Correction
**"Remove the batch effect before DE"** -> Almost always WRONG. Include batch as a covariate in the design formula (`~ batch + condition`) so DESeq2/edgeR/limma model it without subtracting. Subtraction is for visualization only.
## The Single Most Important Modern Insight -- The Nygaard 2016 cardinal sin
Nygaard, Rødland, Hovig 2016 *Biostatistics* 17(1):29-39, "Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses." Translation: **never run ComBat (or ComBat-seq, or `removeBatchEffect`, or SVA-subtract-then-test) and then run DE on the corrected matrix.**
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How to install
mdr add fridrichmethod/awesome-skills/bio-differential-expression-batch-correction@sha256:7f0f86f14b42162eThe line at the top of this page pins the label git:20261018.db2b2b5, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_7b564mild5emc2dj)
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The registry has recorded 1 version of this file, committed on Oct 18, 2026.
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Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_7b564mild5emc2dj GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-differential-expression-batch-correction GET https://markdownregistry.com/api/v1/blob/7f0f86f14b42162e41afc06c07661efecf75f5fbdd502356dc413166d38982c0
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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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