IDEAS home Printed from https://ideas.repec.org/p/osf/metaar/pkqdx.html
   My bibliography  Save this paper

On the optimistic performance evaluation of newly introduced bioinformatic methods

Author

Listed:
  • Buchka, Stefan
  • Hapfelmeier, Alexander
  • Gardner, Paul P
  • Wilson, Rory
  • Boulesteix, Anne-Laure

Abstract

Most research articles presenting new data analysis methods claim that “the new method performs better than existing methods”, but the veracity of such statements is questionable. Our manuscript discusses and illustrates consequences of the optimistic bias occurring during the evaluation of novel data analysis methods, that is, all biases resulting from, for example, selection of datasets or competing methods; better ability to fix bugs in a preferred method; and selective reporting of method variants. We quantitatively investigate this bias using a topical example from epigenetic analysis: normalization methods for data generated by the Illumina HumanMethylation450K BeadChip microarray.

Suggested Citation

  • Buchka, Stefan & Hapfelmeier, Alexander & Gardner, Paul P & Wilson, Rory & Boulesteix, Anne-Laure, 2021. "On the optimistic performance evaluation of newly introduced bioinformatic methods," MetaArXiv pkqdx, Center for Open Science.
    • Handle: RePEc:osf:metaar:pkqdx
    DOI: 10.31219/osf.io/pkqdx
    as

    Download full text from publisher

    File URL: https://osf.io/download/6006eb51ba010908098915d7/
    Download Restriction: no
    File URL: https://libkey.io/10.31219/osf.io/pkqdx?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Kenneth F Schulz & Douglas G Altman & David Moher & for the CONSORT Group, 2010. "CONSORT 2010 Statement: Updated Guidelines for Reporting Parallel Group Randomised Trials," PLOS Medicine, Public Library of Science, vol. 7(3), pages 1-7, March.
    2. Anne-Laure Boulesteix & Sabine Lauer & Manuel J A Eugster, 2013. "A Plea for Neutral Comparison Studies in Computational Sciences," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-11, April.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Theresa Ullmann & Anna Beer & Maximilian Hünemörder & Thomas Seidl & Anne-Laure Boulesteix, 2023. "Over-optimistic evaluation and reporting of novel cluster algorithms: an illustrative study," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 17(1), pages 211-238, March.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Ángel Enrique & Juana Bretón-López & Guadalupe Molinari & Rosa M. Baños & Cristina Botella, 2018. "Efficacy of an adaptation of the Best Possible Self intervention implemented through positive technology: a randomized control trial," Applied Research in Quality of Life, Springer;International Society for Quality-of-Life Studies, vol. 13(3), pages 671-689, September.
    2. Gerben ter Riet & Paula Chesley & Alan G Gross & Lara Siebeling & Patrick Muggensturm & Nadine Heller & Martin Umbehr & Daniela Vollenweider & Tsung Yu & Elie A Akl & Lizzy Brewster & Olaf M Dekkers &, 2013. "All That Glitters Isn't Gold: A Survey on Acknowledgment of Limitations in Biomedical Studies," PLOS ONE, Public Library of Science, vol. 8(11), pages 1-6, November.
    3. Spyridon N Papageorgiou & Georgios N Antonoglou & George K Sándor & Theodore Eliades, 2017. "Randomized clinical trials in orthodontics are rarely registered a priori and often published late or not at all," PLOS ONE, Public Library of Science, vol. 12(8), pages 1-13, August.
    4. Eun-Hi Kong & Myoungsuk Kim & Seonho Kim, 2021. "Effects of a Web-Based Educational Program Regarding Physical Restraint Reduction in Long-Term Care Settings on Nursing Students: A Cluster Randomized Controlled Trial," IJERPH, MDPI, vol. 18(13), pages 1-10, June.
    5. Stavros Petrou & Oliver Rivero-Arias & Helen Dakin & Louise Longworth & Mark Oppe & Robert Froud & Alastair Gray, 2015. "Preferred Reporting Items for Studies Mapping onto Preference-Based Outcome Measures: The MAPS Statement," Medical Decision Making, , vol. 35(6), pages 1-8, August.
    6. Alexander P. L. Martindale & Benjamin Ng & Victoria Ngai & Aditya U. Kale & Lavinia Ferrante di Ruffano & Robert M. Golub & Gary S. Collins & David Moher & Melissa D. McCradden & Lauren Oakden-Rayner , 2024. "Concordance of randomised controlled trials for artificial intelligence interventions with the CONSORT-AI reporting guidelines," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    7. Maria Giné-Garriga & Carme Martin-Borràs & Anna Puig-Ribera & Carlos Martín-Cantera & Mercè Solà & Antonio Cuesta-Vargas & on behalf of the PPAF Group, 2013. "The Effect of a Physical Activity Program on the Total Number of Primary Care Visits in Inactive Patients: A 15-Month Randomized Controlled Trial," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-8, June.
    8. Nahid Norouzi-Gheidari & Alejandro Hernandez & Philippe S. Archambault & Johanne Higgins & Lise Poissant & Dahlia Kairy, 2019. "Feasibility, Safety and Efficacy of a Virtual Reality Exergame System to Supplement Upper Extremity Rehabilitation Post-Stroke: A Pilot Randomized Clinical Trial and Proof of Principle," IJERPH, MDPI, vol. 17(1), pages 1-11, December.
    9. Juliusz Huber & Katarzyna Kaczmarek & Katarzyna Leszczyńska & Przemysław Daroszewski, 2022. "Post-Stroke Treatment with Neuromuscular Functional Electrostimulation of Antagonistic Muscles and Kinesiotherapy Evaluated with Electromyography and Clinical Studies in a Two-Month Follow-Up," IJERPH, MDPI, vol. 19(2), pages 1-17, January.
    10. Süreyya Kılıç & Sema Dereli Yılmaz, 2023. "Virtual Reality Headset Simulating a Nature Environment to Improve Health Outcomes in Pregnant Women: A Randomized-Controlled Trial," Clinical Nursing Research, , vol. 32(8), pages 1104-1114, November.
    11. Denise Howel & Suzanne Moffatt & Catherine Haighton & Andrew Bryant & Frauke Becker & Melanie Steer & Sarah Lawson & Terry Aspray & Eugene M G Milne & Luke Vale & Elaine McColl & Martin White, 2019. "Does domiciliary welfare rights advice improve health-related quality of life in independent-living, socio-economically disadvantaged people aged ≥60 years? Randomised controlled trial, economic and p," PLOS ONE, Public Library of Science, vol. 14(1), pages 1-31, January.
    12. Reynolds, J.P. & Pilling, M. & Marteau, T.M., 2018. "Communicating quantitative evidence of policy effectiveness and support for the policy: Three experimental studies," Social Science & Medicine, Elsevier, vol. 218(C), pages 1-12.
    13. Marlene De Fabritiis & Federica Trisolini & Gloria Bertuletti & Ionut Daniel Fagadau & Davide Ginelli & Katiuscia Pia Lalopa & Lisa Peverelli & Alessia Pirola & Gaia Sala & Marta Maisto & Fabio Madedd, 2022. "An Internet-Based Multi-Approach Intervention Targeting University Students Suffering from Psychological Problems: Design, Implementation, and Evaluation," IJERPH, MDPI, vol. 19(5), pages 1-15, February.
    14. Andreas C Drichoutis & Rodolfo M Nayga, 2020. "Economic Rationality under Cognitive Load," The Economic Journal, Royal Economic Society, vol. 130(632), pages 2382-2409.
    15. Natalia Stanulewicz & Emily Knox & Melanie Narayanasamy & Noureen Shivji & Kamlesh Khunti & Holly Blake, 2019. "Effectiveness of Lifestyle Health Promotion Interventions for Nurses: A Systematic Review," IJERPH, MDPI, vol. 17(1), pages 1-36, December.
    16. Jörg Peters & Jörg Langbein & Gareth Roberts, 2018. "Generalization in the Tropics – Development Policy, Randomized Controlled Trials, and External Validity," The World Bank Research Observer, World Bank, vol. 33(1), pages 34-64.
    17. Jonas Czwikla & Alexandra Herzberg & Sonja Kapp & Stephan Kloep & Heinz Rothgang & Ina Nitschke & Cornelius Haffner & Falk Hoffmann, 2021. "Effectiveness of a Dental Intervention to Improve Oral Health among Home Care Recipients: A Randomized Controlled Trial," IJERPH, MDPI, vol. 18(17), pages 1-13, September.
    18. Yuan Sheng & Li-Hong Yang & Yan Wu & Wei Gao & Sheng-Yi Dongye, 2024. "Implementation of Tunneled Peripherally Inserted Central Catheters Placement in Cancer Patients: A Randomized Multicenter Study," Clinical Nursing Research, , vol. 33(1), pages 19-26, January.
    19. Maria Paula Valk-Draad & Sabine Bohnet-Joschko, 2022. "Nursing Home-Sensitive Hospitalizations and the Relevance of Telemedicine: A Scoping Review," IJERPH, MDPI, vol. 19(19), pages 1-23, October.
    20. Birte Østergaard & Romy Mahrer‐Imhof & Mahdi Shamali & Birgitte Nørgaard & Bernard Jeune & Karen Steenvinkel Pedersen & Jørgen Lauridsen, 2021. "Effect of family nursing therapeutic conversations on patients with heart failure and their family members: Secondary outcomes of a randomised multicentre trial," Journal of Clinical Nursing, John Wiley & Sons, vol. 30(5-6), pages 742-756, March.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:osf:metaar:pkqdx. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: OSF (email available below). General contact details of provider: https://osf.io/preprints/metaarxiv .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.