Repeatability of published microarray gene expression analyses

By John P. A. Ioannidis, David B. Allison, C. Ball, I. Coulibaly, Xiangqin Cui, A. Culhane, M. Falchi, Cesare Furlanello, L. Game, Giuseppe Jurman and 6 more. Nature Genetics, 2009

557 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c1aa3c612e323acc33348c2a706cc7a12941412e

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Citations in the corpus

ArrayExpress update—simplifying data submissions (2014, methodology): “To facilitate reproducible research (4), we promote the data compliance to the Minimum Information About a Microarray Experiment (MIAME) (5) or Minimum Information about Sequencing Experiment (MINSEQE; http: //www.”
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010, background): “Issues that prevented reproduction included missing raw data, details in processing methods (especially computational ones), and software and hardware details [10].”
Reproducibility in Science: Improving the Standard for Basic and Preclinical Research (2015, unknown): “Examples of Some Reported Reproducibility Concerns in Preclinical Studies Author Field Reported Concerns Ioannidis et al (2009)22 Microarray data 16/18 studies unable to be reproduced in principle from raw data Baggerly et al (2009)23 Microarray data Multiple; insufficient data/poor documentation Se”
How Trustworthy Is the Scientific Literature in Industrial and Organizational Psychology? (2013, background): “…from other scientific disciplines indicates that the reproducibility of findings from published articles is shockingly low (e.g., Begley & Ellis, 2012; Ioannidis et al., 2009), likely due to incomplete reporting of relevant statistical information in the published articles (Baggerly, 2010).”
Next-generation sequencing data interpretation: enhancing reproducibility and accessibility (2012, background): “…computational reproducibility are not unique to life sciences; the importance of being able to repeat computational experiments was first brought up in geosciences 38 and became relevant in life sciences following the establishment of microarray technology and high-throughput sequencing 3,39,40 .”
ImmPort: disseminating data to the public for the future of immunology (2014, background): “Ioannidis and others have shown that attempts to reproduce published scientiﬁc ﬁndings from studies using high-throughput molecular measurements fail due to the lack of available data [17].”
The Impact of Class Rebalancing Techniques on the Performance and Interpretation of Defect Prediction Models (2018, background): “[54] raise concerns that the majority of medical”
Standardization of sample collection, isolation and analysis methods in extracellular vesicle research (2013, unknown): “Database submission Data submission is mandated by most journals (95,96) and independent studies have found that unavailability of data is associated with low data or study quality (94, 97,98); however, compliance remains poor (94,99,100).”
FlowRepository: A resource of annotated flow cytometry datasets associated with peer‐reviewed publications (2012, background): “In a recent re-evaluation of 18 peer-reviewed Nature Genetics microarray articles, the inability of researchers to reproduce analyses was directly linked to data unavailability, incomplete data annotation, or speciﬁcation of data processing and analysis (12).”
Reproducibility of computational workflows is automated using continuous analysis (2017, background): “Indeed, Ioannidis et al. 9 showed that the outputs of 56% of microarray gene expression experiments could not be reproduced, and another 33% could be reproduced only with discrepancies.”
Ten Simple Rules for Reproducible Computational Research (2013, background): “…through studies showing that scientific papers commonly leave out experimental details essential for reproduction [5], studies showing difficulties with replicating published experimental results [6], an increase in retracted papers [7], and through a high number of failing clinical trials [8,9].”