Confronting false discoveries in single-cell differential expression.

Jordan W Squair, Matthieu Gautier, Claudia Kathe, Mark A Anderson, Nicholas D James, Thomas H Hutson, Rémi Hudelle, Taha Qaiser, Kaya J E Matson, Quentin Barraud, Ariel J Levine, Gioele La Manno, Michael A Skinnider, Grégoire Courtine

September 2021 Nat Commun

Synopsis of Social media discussions

The discussions highlight the effectiveness of pseudobulk approaches in single-cell differential expression analysis. Phrases like 'must-read paper' and 'obvious but important reminder' indicate the importance users place on the findings, and a phrase like 'save money, save time, save resources' reflects a strong endorsement of its practical benefits. The tone is overwhelmingly positive, indicating both enthusiasm and alignment with the publication's conclusions, while the use of technical commentary showcases deep understanding.

A
Agreement
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The discussions largely support and affirm the publication's findings, indicating strong consensus among contributors.

I
Interest
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Many users express high levels of curiosity and recognize the publication's relevance to their fields.

E
Engagement
 High engagement

Posts delve deeply into specific methodologies and implications, demonstrating thoughtful engagement rather than superficial comments.

I
Impact
 High level of impact

Contributors believe the publication will substantially influence practices in single-cell analysis based on the insights provided.

Social Mentions

YouTube

1 Videos

Bluesky

1 Posts

Facebook

2 Posts

Twitter

100 Posts

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3 Articles

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24

Total Likes

313

Extended Reach

345,396

Social Features

107

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Posts referencing the article

Addressing False Discoveries in Single-Cell Expression Analysis

Addressing False Discoveries in Single-Cell Expression Analysis

Differential expression analysis in single-cell transcriptomics identifies how cell types respond to conditions like diseases and injuries. This video examines the effectiveness of various statistical methods and the risks of biased results arising from biological variation.

STEM RTCL TV

July 2, 2023

24 views

  • Ming "Tommy" Tang
    @tangming2005 (Twitter)

    3/  [Confronting false discoveries in single-cell differential expression](https://t.co/FfUmk03S6X) "These observations suggest that, in practice, pseudobulk approaches provide an excellent trade-off between speed and accuracy for single-cell DE analysis."
    view full post

    April 22, 2025

  • Ming Tommy Tang
    @tommytang.bsky.social (Bluesky)

    3/  [Confronting false discoveries in single-cell differential expression](www.nature.com/articles/s4...) "These observations suggest that, in practice, pseudobulk approaches provide an excellent trade-off between speed and accuracy for single-cell DE analysis."
    view full post

    April 22, 2025

    1

  • Ming "Tommy" Tang
    @tangming2005 (Twitter)

    4/ [Confronting false discoveries in single-cell differential expression](https://t.co/FfUmk03S6X) "These observations suggest that, in practice, pseudobulk approaches provide an excellent trade-off between speed and accuracy for single-cell DE analysis." pseduobulk works well.
    view full post

    July 15, 2024

    4

  • ZheFrench
    @ZheFrench (Twitter)

    Confronting false discoveries in single-cell differential expression https://t.co/6WWbHqO8sB
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    June 16, 2023

    1

  • Sean Simmons
    @seankenneths (Twitter)

    @yogeshgoyallab For references, the paper "confronting false discoveries in single cell differential expression" is probably the one I most believe...
    view full post

    May 13, 2023

  • Yossawat Suwanlikit, MD
    @Yossawat_Suw (Twitter)

    Confronting false discoveries in single-cell differential expression https://t.co/iJpHqJSL7A
    view full post

    March 14, 2023

  • Harim Chun
    @chun_harim (Twitter)

    RT @tangming2005: 3/ [Confronting false discoveries in single-cell differential expression](https://t.co/FfUmk03khp) "These observations s…
    view full post

    February 5, 2023

    3

  • Raúl Jiménez Castaño
    @ruljc (Twitter)

    RT @tangming2005: 3/ [Confronting false discoveries in single-cell differential expression](https://t.co/FfUmk03khp) "These observations s…
    view full post

    December 15, 2022

    3

  • Suren Neupane
    @SurenNeupane1 (Twitter)

    RT @tangming2005: 3/ [Confronting false discoveries in single-cell differential expression](https://t.co/FfUmk03khp) "These observations s…
    view full post

    December 14, 2022

    3

  • Ming "Tommy" Tang
    @tangming2005 (Twitter)

    3/ [Confronting false discoveries in single-cell differential expression](https://t.co/FfUmk03khp) "These observations suggest that, in practice, pseudobulk approaches provide an excellent trade-off between speed and accuracy for single-cell DE analysis.
    view full post

    December 14, 2022

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  • Abigail Mackey
    @AbigailMackey1 (Twitter)

    @keviniwatt @grith_hojfeldt "failing to account for biological replicates causes single-cell methods to systematically underestimate the variance of gene expression" Nat Comm 2021 no kidding... https://t.co/jpPAdkj60k
    view full post

    September 28, 2022

  • Aurora
    @auroratummy (Twitter)

    シングルセル解析で発現変動解析をする際によく使われるWilcoxonの順位和検定は、サンプル (e.g. 由来組織) 間で分散の大きい遺伝子を誤ってDEGとして検出するバイアスがある。 Confronting false discoveries in single-cell differential expression https://t.co/zHIkfxsh6a
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    December 13, 2021

    1

  • ashish (@acgt01@genomic.social)
    @acgt01 (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    November 3, 2021

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  • Thomas Walle
    @science_wallet (Twitter)

    Obvious but important reminder. Single cells from one individual are not statistically independent. Hence, p values from methods assuming this e.g. Mann-Whitney U are meaningless... https://t.co/a34x2SBChE
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    November 2, 2021

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  • ning
    @notningyuan (Twitter)

    Super interesting stuff. Squair et al. demonstrate scRNA-seq DE methods which aggregate-then-compare perform better than cell-by-cell comparison methods, because they better account for variance in biological replicates (63/n) https://t.co/5VShi71kfe
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    November 2, 2021

  • Jordan Russell, Ph.D
    @russelltyjor (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 16, 2021

    29

  • Brendan Miller
    @_brendanmiller_ (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
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    October 16, 2021

    29

  • Yingying Cao
    @yingyingcaoyyc (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 16, 2021

    29

  • B B
    @bblr01 (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 16, 2021

    29

  • Yunze Liu
    @ReedLiu1314 (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
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    October 16, 2021

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  • Single Cell Media
    @SingleCellMedia (Twitter)

    RT @nibras_issa: Confronting false discoveries in single-cell differential expression | Nature Communications مهم جداً للمهتم ب scRNA htt…
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    October 16, 2021

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  • Nabras Almahrami
    @nibras_issa (Twitter)

    Confronting false discoveries in single-cell differential expression | Nature Communications مهم جداً للمهتم ب scRNA https://t.co/82gUJXvI5H
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    October 16, 2021

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  • Eisa Mahyari Ph.D.
    @eisamahyari (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 16, 2021

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  • Mandhri Abeysooriy
    @MandhriAbeysoo1 (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 16, 2021

    29

  • Daniel Beiting
    @hostmicrobe (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 16, 2021

    29

  • Chloe
    @goldsmith_chloe (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 15, 2021

    29

  • a.khmelevskaya
    @khmelevskaya_a (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 15, 2021

    29

  • Carlos E Alvarez
    @CarlosEAlvare17 (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 15, 2021

    29

  • Tim Shaw
    @gatechatl (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 15, 2021

    29

  • Drake Williams
    @drake_dds (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 15, 2021

    29

  • Ana Viñuela
    @anavinuela (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 15, 2021

    29

  • Alejandro Montenegro
    @aemonten (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 15, 2021

    29

  • Nicolas Robine
    @notSoJunkDNA (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 15, 2021

    29

  • elaina graham
    @perilousUnknown (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 15, 2021

    29

  • Vijay Sankaran
    @bloodgenes (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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    October 15, 2021

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  • Gaurav Chatterjee
    @Gaurav_C42 (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 15, 2021

    29

  • Mick W@tson ↙️
    @BioMickWatson (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 15, 2021

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  • Yunpeng Liu-Lupo
    @leciel199071 (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 15, 2021

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  • Mark Borris Aldonza (@precursorcell.bsky.social
    @PrecursorCell (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 15, 2021

    29

  • 田口善弘＠発言は私の個人としての見解であり中央大学やその機関の意見を代表するものではありません
    @Yh_Taguchi (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
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    October 15, 2021

    29

  • Mari Miyamoto
    @marimiya_tky (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
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    October 15, 2021

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  • Rishikesh Gupta, Ph.D.
    @its_rkgupta (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
    view full post

    October 15, 2021

    29

  • Sagiv Shifman
    @SagivShifman (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
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    October 15, 2021

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  • Single Cell Media
    @SingleCellMedia (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
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    October 14, 2021

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  • Bioinformatics Trends 
    @BinfoTrends (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
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    October 14, 2021

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  • CompChemBio Bot
    @CompChemBioBot (Twitter)

    RT @NhiHin: Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell…
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    October 14, 2021

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  • Nhi Hin
    @NhiHin (Twitter)

    Must-read paper for those working with #scRNAseq showing that pseudobulk methods (limma, edgeR) outperform popular #singlecell methods like Wilcoxon test: Confronting false discoveries in single-cell differential expression https://t.co/mFvqXf7Kv4 #bioinformatics @wessidepraxis
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    October 14, 2021

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  • David Russler-Germain, MD/PhD
    @dgermain21 (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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    @AnnaEnim (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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    @SchneiderChrisG (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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    October 12, 2021

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    @filimasini (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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    October 9, 2021

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  • Ignacy Bonter
    @Ignacybo (Twitter)

    RT @LGMartelotto: Confronting false discoveries in single-cell differential expression | Nature Communications https://t.co/pqnzJdiazZ
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    October 8, 2021

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  • Arthur Liberzon
    @arthlib (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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    October 8, 2021

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    @ZDQ_Interlaken (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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  • The()Graduate
    @firexgamerx (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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    October 8, 2021

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  • Single Cell Media
    @SingleCellMedia (Twitter)

    RT @SusanneLorenz77: Confronting false discoveries in single-cell differential expression. https://t.co/NFrZRim3FU
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    October 8, 2021

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  • Susanne Lorenz
    @SusanneLorenz77 (Twitter)

    Confronting false discoveries in single-cell differential expression. https://t.co/NFrZRim3FU
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    October 8, 2021

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    @rio_sugimura (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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    October 7, 2021

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    @KentWillisMD (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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    October 7, 2021

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  • Andres F. Cardona
    @AndresFCardonaZ (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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  • Ben Hogan
    @BenjaminHogan13 (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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  • Functional Genomics Core Facility (FGCF)
    @FunGenCore (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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  • Zulfikar Azam
    @ZulfikarAzam10 (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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    @fbsisti (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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  • protocols.io
    @protocolsIO (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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  • Jake Reske
    @reskejak (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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    October 7, 2021

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  • Ana Amorim
    @AnaAmor41170370 (Twitter)

    RT @MartinUCSF: Confronting false discoveries in single-cell differential expression https://t.co/vDVBXPoOtb
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    October 7, 2021

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  • Dr. Abbas
    @Abbas514G (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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  • Juan C. Nieto
    @jc_nietos (Twitter)

    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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    October 7, 2021

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  • Daniel Lee
    @zzzang5889 (Twitter)

    RT @MartinUCSF: Confronting false discoveries in single-cell differential expression https://t.co/vDVBXPoOtb
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    October 7, 2021

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  • Single Cell Media
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    RT @LGMartelotto: Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries i…
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  • Santiago Carmona
    @carmonation (Twitter)

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    October 7, 2021

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  • Luciano Martelotto
    @LGMartelotto (Twitter)

    Reposting this again…save money, save time, save resources, make discoveries that last. Confronting false discoveries in single-cell differential expression | Nature Communications https://t.co/pqnzJd0zIr
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  • Claudia Cantoni
    @Clodida (Twitter)

    RT @MartinUCSF: Confronting false discoveries in single-cell differential expression https://t.co/vDVBXPoOtb
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    October 7, 2021

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  • Yvon Woappi
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    RT @MartinUCSF: Confronting false discoveries in single-cell differential expression https://t.co/vDVBXPoOtb
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  • Manni Adam
    @6degreesofManni (Twitter)

    RT @MartinUCSF: Confronting false discoveries in single-cell differential expression https://t.co/vDVBXPoOtb
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  • Holly Ingraham
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    RT @MartinUCSF: Confronting false discoveries in single-cell differential expression https://t.co/vDVBXPoOtb
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  • Allison May, MD
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    RT @jsantoyo: Confronting false discoveries in single-cell differential expression. #SingleCell #DE #BiologicalReplicatesVariation #BiasedR…
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    October 6, 2021

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    RT @SENGLAITAN: Confronting false discoveries in single-cell differential expression https://t.co/T9CYw38hZm
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  • Single Cell Media
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    RT @Pluchinolab: Confronting false discoveries in single-cell differential expression | Nature Communications https://t.co/yGrCHxQUnB
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  • Pluchino lab - Regenerative Neuroimmunology
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    Confronting false discoveries in single-cell differential expression | Nature Communications https://t.co/yGrCHxQUnB
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    RT @MartinUCSF: Confronting false discoveries in single-cell differential expression https://t.co/vDVBXPoOtb
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    RT @MartinUCSF: Confronting false discoveries in single-cell differential expression https://t.co/vDVBXPoOtb
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  • Saeed Salehin Akhand
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    RT @SENGLAITAN: Confronting false discoveries in single-cell differential expression https://t.co/T9CYw38hZm
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  • Matt Callahan
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    RT @MartinUCSF: Confronting false discoveries in single-cell differential expression https://t.co/vDVBXPoOtb
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    RT @MartinUCSF: Confronting false discoveries in single-cell differential expression https://t.co/vDVBXPoOtb
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  • Ela W. Contreras Panta
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    RT @LGMartelotto: Confronting false discoveries in single-cell differential expression | Nature Communications https://t.co/pqnzJdiazZ
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    RT @MartinUCSF: Confronting false discoveries in single-cell differential expression https://t.co/vDVBXPoOtb
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    RT @LGMartelotto: Confronting false discoveries in single-cell differential expression | Nature Communications https://t.co/pqnzJdiazZ
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  • Martin Kampmann
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    RT @LGMartelotto: Confronting false discoveries in single-cell differential expression | Nature Communications https://t.co/pqnzJdiazZ
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    RT @SENGLAITAN: Confronting false discoveries in single-cell differential expression https://t.co/T9CYw38hZm
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    RT @SENGLAITAN: Confronting false discoveries in single-cell differential expression https://t.co/T9CYw38hZm
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  • Marcel Schulz - @marcelschulz@genomic.social
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    RT @LGMartelotto: Confronting false discoveries in single-cell differential expression | Nature Communications https://t.co/pqnzJdiazZ
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  • Kévin Lebrigand, PhD
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    RT @LGMartelotto: Confronting false discoveries in single-cell differential expression | Nature Communications https://t.co/pqnzJdiazZ
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  • zhenyang
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  • Tamas Schauer
    @tamas_schauer (Twitter)

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  • Inspecting Immunology
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  • Sanju Sinha
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    @ralzahrani2020 (Twitter)

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Abstract Synopsis

  • Differential expression analysis in single-cell transcriptomics helps identify how different cell types respond to conditions like diseases and injuries.
  • Many statistical methods exist for finding differentially expressed genes, but their effectiveness varies based on how well they handle variation between biological samples.
  • Ignoring biological variation can lead to biased results and false discoveries, as demonstrated by examining gene expression in injured mouse spinal cords.