ScientificInquiry_ExpDesign/index.Rmd at main · fmicompbio/ScientificInquiry_ExpDesign · GitHub

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---
title: "Scientific Inquiry - Experimental design session 2026"
output:
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---

This page contains links to material for the experimental design session of the FMI Scientific Inquiry course 2026.

* [Slides Charlotte](slides/)
* [Slides Michael (PDF)](MStadler_ScientificInquiry_Part2_2025.pdf)
* [Exercises on confounding (for self-study)](expdesign_practical.html)
* [Notes on design matrices (for self-study)](design_matrices.html)

<hr>

# Resources

[**Nature Methods 'Statistics for Biologists' collection**](https://www.nature.com/collections/qghhqm):

* [N Altman & M Krzywinski: Sources of variation. _Nat Methods_ 12:5-6 (2015)](https://www.nature.com/articles/nmeth.3224)
* [M Krzywinski & N Altman: Designing comparative experiments. _Nat Methods_ 11:597-598 (2014)](https://www.nature.com/articles/nmeth.2974)
* [M Krzywinski & N Altman: Analysis of variance and blocking. _Nat Methods_ 11:699-700 (2014)](https://www.nature.com/articles/nmeth.3005)
* [P Blainey, M Krzywinski & N Altman: Replication. _Nat Methods_ 11:879-880 (2014)](https://www.nature.com/articles/nmeth.3091)
* [M Krzywinski, N Altman & P Blainey: Nested designs _Nat Methods_ 11:977-978 (2014)](https://www.nature.com/articles/nmeth.3137)
* [M Krzywinski & N Altman: Two-factor designs. _Nat Methods_ 11:1187-1188 (2014)](https://www.nature.com/articles/nmeth.3180)

**Other relevant material**:

* [Slide deck from Susan Holmes and Wolfgang Huber on Experimental Design](https://www.huber.embl.de/users/whuber/2301-GHGA-best-analysis-practices/design.html#/title-slide)
* [R package containing a shiny app to explore confounding and different experimental designs](https://csoneson.github.io/ConfoundingExplorer/)

* [A blog post about interpreting p-value histograms](http://varianceexplained.org/statistics/interpreting-pvalue-histogram/)

* [MR Wagner & M Kleiner: How thoughtful experimental design can empower biologists in the omics era](https://www.nature.com/articles/s41467-025-62616-x)

* [M Baker: 1,500 scientists lift the lid on reproducibility. _Nature_ 533:452–454 (2016)](https://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970)
* [LB Sheiner: Learning vs confirming in clinical drug development. _Clinical Pharmacology and Therapeutics_ 61(3):275-291 (1997)](https://ascpt.onlinelibrary.wiley.com/doi/abs/10.1016/S0009-9236%2897%2990160-0)
* [PL Auer & RW Doerge: Statistical design and analysis of RNA sequencing data. _Genetics_ 185(2):405-416 (2010)](https://www.genetics.org/content/185/2/405)
* [SE Lazic: Experimental design for laboratory biologists. _Cambridge University Press_ (2016)](https://stanlazic.github.io/EDLB.html)
* [SE Lazic et al: What exactly is ‘N’ in cell culture and animal experiments? _PLoS Biol_ 16(4): e2005282 (2018)](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005282)
* [P Norvig: Warning signs in experimental design and interpretation](https://norvig.com/experiment-design.html)
* [JT Leek et al: Tackling the widespread and critical impact of batch effects in high-throughput data. _Nature Reviews Genetics_ 11:733–739 (2010)](https://www.nature.com/articles/nrg2825)
* [MJ Larsen et al: Microarray-Based RNA Profiling of Breast Cancer: Batch Effect Removal Improves Cross-Platform Consistency. _Biomed Res Int_ 2014: 651751 (2014)](https://www.hindawi.com/journals/bmri/2014/651751/)
* [S Lin et al: Comparison of the transcriptional landscapes between human and mouse tissues. _PNAS_ 111(48):17224-17229 (2014)](https://www.pnas.org/content/111/48/17224)
* [Y Gilad & O Mizrahi-Man: A reanalysis of mouse ENCODE comparative gene expression data. _F1000Research_ 4:121 (2015)](https://f1000research.com/articles/4-121/v1)
* [J Hu et al: The importance of experimental design in proteomic mass spectrometry experiments: Some cautionary tales. _Briefings in Functional Genomics_ 3(4):322–331 (2005)](https://academic.oup.com/bfg/article/3/4/322/197822)
* [B Klaus: Statistical relevance - relevant statistics, part I. _EMBO Journal_ 34:2727-2730 (2015)](https://www.embopress.org/doi/full/10.15252/embj.201592958)

### Archive

[2025](2025/index.html)<br>
[2024](2024/index.html)