prevention approach Jeffrey T. Leeka,1 and Roger D. Pengb aAssociate Professor of Biostatistics and Oncology and bAssociate Professor of Biostatistics, Johns Hopkins University, Baltimore, MD Reproducibility—the ability to recompute results—and replicability—the chances other experimenters will achieve a consistent result—are two foundational characteristics of successful scientific research. Consistent findings from independent investigators are the primary means by which scientific evidence accumulates for or against a hy- pothesis. Yet, of late, there has been a crisis of confidence among researchers worried about the rate at which studies are either reproducible or replicable. To maintain the integrity of science research and the public’s trust in science, the scientific community must ensure reproducibility and replicability by engaging in a more preventative ap- proach that greatly expands data analysis education and routinely uses software tools. We define reproducibility as the ability to recompute data analytic results given an observed dataset and knowledge of the data analysis pipeline. The replicability of a study been some very public failings of reproduc- ibility across a range of disciplines from can- cer genomics (3) to economics (4), and the data for many publications have not been made publicly available, raising doubts about the quality of data analyses. Popular press articles have raised questions about the reproducibility of all scientific research (5), and the US Congress has convened hearings focused on the transparency of scientific re- search (6). The result is that much of the scientific enterprise has been called into question, putting funding and hard won sci- entific truths at risk. From a computational perspective, there are three major components to a reproducible and replicable study: (i) the raw data from the experiment are available, (ii) the statisti- cal code and documentation to reproduce the analysis are available, and (iii) a correct data analysis must be performed. Recent cultural shifts in genomics and other areas have had computational tools such as knitr, iPython notebook, LONI, and Galaxy (8) have simplified the process of distributing repro- ducible data analyses. Unfortunately, the mere reproducibility of computational results is insufficient to ad- dress the replication crisis because even a re- producible analysis can suffer from many problems—confounding from omitted varia- bles, poor study design, missing data—that threaten the validity and useful interpretation of the results. Although improving the repro- ducibility of research may increase the rate at which flawed analyses are uncovered, as recent high-profile examples have demon- strated (4), it does not change the fact that problematic research is conducted in the first place. The key question we want to answer when seeing the results of any scientific study is “Can I trust this data analysis?” If we think of problematic data analysis as a disease, repro- ducibility speeds diagnosis and treatment in the form of screening and rejection of poor data analyses by referees, editors, and other scientists in the community (Fig. 1). OPINION education and routinely uses software tools. We define reproducibility as the ability to recompute data analytic results given an observed dataset and knowledge of the data analysis pipeline. The replicability of a study is the chance that an independent experi- ment targeting the same scientific question will produce a consistent result (1). Con- cerns among scientists about both have gained significant traction recently due in part to a statistical argument that suggested most published scientific results may be false positives (2). At the same time, there have the experiment are available, (ii) the statisti- cal code and documentation to reproduce the analysis are available, and (iii) a correct data analysis must be performed. Recent cultural shifts in genomics and other areas have had a positive impact on data and code availabil- ity. Journals are starting to require data avail- ability as a condition for publication (7), and centralized databases such as the National Center for Biotechnology Information’s Gene Expression Omnibus are being cre- ated for depositing data generated by pub- licly funded scientific experiments. New problematic data a ducibility speeds d the form of screen data analyses by r scientists in the co This medicatio quality relies on p to make this diagn is a tall order. Edi medical and scie the training and evaluation of a da is compounded b and data analyse ingly complex, th journals continu the demands on are increasing. T duced the efficac tifying and cor discoveries in the cially, the medic address the probl We suggest that to be considered Fig. 1. Peer review and editor evaluation help treat poor data analysis. Education and evidence-based data analysis can be thought of as preventative measures. Author contributions: J.T.L. 1To whom correspondence edu. Any opinions, findings, con pressed in this work are tho reflect the views of the Na www.pnas.org/cgi/doi/10.1073/pnas.1421412111 PNAS | February 10, 2015 |
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