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Good statistical practice in pharmacology. Problem 1.

ABSTRACT: BACKGROUND AND PURPOSE: This paper is intended to assist pharmacologists in making the most of statistical analysis and in avoiding common errors that can lead to false conclusions. APPROACH: A scenario is presented where a pathway inhibitor increased blood pressure responses to an agonist by about one third. The fictional experimenter concludes that the inhibitor enhanced the responses to the agonist, but has not applied any statistical analysis. Questions are asked of the reader, and a discussion of the author's answers is presented. RESULTS: The agonist responses have unequal standard errors, as often seen in data like these concentration-response curves with responses expressed as change from baseline. The uneven variability (heteroscedasticity) violates an assumption of conventional parametric statistical analyses, but can be corrected by data transformation. Expressing the data as absolute blood pressure and then transforming it to log blood pressure eliminated the heteroscedasticity, but made evident an effect of the inhibitor on baseline blood pressure. CONCLUSIONS AND IMPLICATIONS: Statistical analysis is a sensible precaution against mistakes, but cannot protect against all erroneous conclusions. In this scenario, the inhibitor reduced the blood pressure and increased responses to the agonist. However, it is likely that the latter effect was a consequence of the former and thus no conclusion can be safely drawn about any direct interaction between the agonist and the pathway inhibitor from this experiment. Where results are awkward to interpret because of confounding factors such as an altered baseline, statistical analysis may not be very useful in supporting a safe conclusion.

SUBMITTER: Lew M

PROVIDER: S-EPMC2042955 | biostudies-other | 2007 Oct

REPOSITORIES: biostudies-other

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Project description:BackgroundThe Health Information Technology for Economic and Clinical Health Act (HITECH) has greatly accelerated the adoption of electronic health records (EHRs) with the promise of better clinical decisions and patients' outcomes. One of the core criteria for "Meaningful Use" of EHRs is to have a problem list that shows the most important health problems faced by a patient. The implementation of problem lists in EHRs has a potential to help practitioners to provide customized care to patients. However, it remains an open question on how to leverage problem lists in different practice settings to provide tailored care, of which the bottleneck lies in the associations between problem list and practice setting.MethodsIn this study, using sampled clinical documents associated with a cohort of patients who received their primary care at Mayo Clinic, we investigated the associations between problem list and practice setting through natural language processing (NLP) and topic modeling techniques. Specifically, after practice settings and problem lists were normalized, statistical χ2 test, term frequency-inverse document frequency (TF-IDF) and enrichment analysis were used to choose representative concepts for each setting. Then Latent Dirichlet Allocations (LDA) were used to train topic models and predict potential practice settings using similarity metrics based on the problem concepts representative of practice settings. Evaluation was conducted through 5-fold cross validation and Recall@k, Precision@k and F1@k were calculated.ResultsOur method can generate prioritized and meaningful problem lists corresponding to specific practice settings. For practice setting prediction, recall increases from 0.719 (k = 2) to 0.931 (k = 10), precision increases from 0.882 (k = 2) to 0.931 (k = 10) and F1 increases from 0.790 (k = 2) to 0.931 (k = 10).ConclusionTo our best knowledge, our study is the first attempting to discover the association between the problem lists and hospital practice settings. In the future, we plan to investigate how to provide more tailored care by utilizing the association between problem list and practice setting revealed in this study.

Project description:Introduction: Publications arguing against the null hypothesis significance testing (NHST) procedure and in favor of good statistical practices have increased. The most frequently mentioned alternatives to NHST are effect size statistics (ES), confidence intervals (CIs), and meta-analyses. A recent survey conducted in Spain found that academic psychologists have poor knowledge about effect size statistics, confidence intervals, and graphic displays for meta-analyses, which might lead to a misinterpretation of the results. In addition, it also found that, although the use of ES is becoming generalized, the same thing is not true for CIs. Finally, academics with greater knowledge about ES statistics presented a profile closer to good statistical practice and research design. Our main purpose was to analyze the extension of these results to a different geographical area through a replication study. Methods: For this purpose, we elaborated an on-line survey that included the same items as the original research, and we asked academic psychologists to indicate their level of knowledge about ES, their CIs, and meta-analyses, and how they use them. The sample consisted of 159 Italian academic psychologists (54.09% women, mean age of 47.65 years). The mean number of years in the position of professor was 12.90 (SD = 10.21). Results: As in the original research, the results showed that, although the use of effect size estimates is becoming generalized, an under-reporting of CIs for ES persists. The most frequent ES statistics mentioned were Cohen's d and R2/?2, which can have outliers or show non-normality or violate statistical assumptions. In addition, academics showed poor knowledge about meta-analytic displays (e.g., forest plot and funnel plot) and quality checklists for studies. Finally, academics with higher-level knowledge about ES statistics seem to have a profile closer to good statistical practices. Conclusions: Changing statistical practice is not easy.This change requires statistical training programs for academics, both graduate and undergraduate.

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Good statistical practice in pharmacology. Problem 1.

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