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NITPicker: selecting time points for follow-up experiments.

ABSTRACT: BACKGROUND:The design of an experiment influences both what a researcher can measure, as well as how much confidence can be placed in the results. As such, it is vitally important that experimental design decisions do not systematically bias research outcomes. At the same time, making optimal design decisions can produce results leading to statistically stronger conclusions. Deciding where and when to sample are among the most critical aspects of many experimental designs; for example, we might have to choose the time points at which to measure some quantity in a time series experiment. Choosing times which are too far apart could result in missing short bursts of activity. On the other hand, there may be time points which provide very little information regarding the overall behaviour of the quantity in question. RESULTS:In this study, we develop a tool called NITPicker (Next Iteration Time-point Picker) for selecting optimal time points (or spatial points along a single axis), that eliminates some of the biases caused by human decision-making, while maximising information about the shape of the underlying curves. NITPicker uses ideas from the field of functional data analysis. NITPicker is available on the Comprehensive R Archive Network (CRAN) and code for drawing figures is available on Github ( https://github.com/ezer/NITPicker ). CONCLUSIONS:NITPicker performs well on diverse real-world datasets that would be relevant for varied biological applications, including designing follow-up experiments for longitudinal gene expression data, weather pattern changes over time, and growth curves.

SUBMITTER: Ezer D

PROVIDER: S-EPMC6444531 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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NITPicker: selecting time points for follow-up experiments.

Ezer Daphne D Keir Joseph J

BMC bioinformatics 20190402 1

<h4>Background</h4>The design of an experiment influences both what a researcher can measure, as well as how much confidence can be placed in the results. As such, it is vitally important that experimental design decisions do not systematically bias research outcomes. At the same time, making optimal design decisions can produce results leading to statistically stronger conclusions. Deciding where and when to sample are among the most critical aspects of many experimental designs; for example, w ...[more]

PMID: 30940082

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Project description:BackgroundRheumatic diseases commonly affect joints and other structures in the hand. Surgery is a traditional way to treat hand problems in inflammatory rheumatic diseases with the purposes of pain relief, restore function and prevent progression. There are numerous measures to choose from, and a combination of outcome measures is recommended. This study evaluated if instruments commonly used in rheumatologic clinical practice are suitable to measure outcome of hand surgery and to identify time points relevant for follow-up.MethodsThirty-one patients (median age 56 years, median disease duration 15 years) with inflammatory rheumatic disease and need for post-surgical occupational therapy intervention formed this pilot study group. Hand function was assessed regarding grip strength (Grippit), pain (VAS), range of motion (ROM) (Signals of Functional Impairment (SOFI)) and grip ability (Grip Ability Test (GAT)). Activities of daily life (ADL) were assessed by means of Disabilities of the Arm, Shoulder and Hand Outcome (DASH) and Canadian Occupational Performance Measure (COPM). The instruments were evaluated by responsiveness and feasibility; follow-up points were 0, 3, 6 and 12 months.ResultsAll instruments showed significant change at one or more follow-up points. Satisfaction with activities (COPM) showed the best responsiveness (SMR>0.8), while ROM measured with SOFI had low responsiveness at most follow-up time points. The responsiveness of the instruments was stable between 6 and 12 month follow-up which imply that 6 month is an appropriate time for evaluating short-term effect of hand surgery in rheumatic diseases.ConclusionWe suggest a core set of instruments measuring pain, grip strength, grip ability, perceived symptoms and self-defined daily activities. This study has shown that VAS pain, the Grippit instrument, GAT, DASH symptom scale and COPM are suitable outcome instruments for hand surgery, while SOFI may be a more insensitive test. However, the feasibility of this protocol in clinical practice awaits prospective studies.

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NITPicker: selecting time points for follow-up experiments.

Publications

NITPicker: selecting time points for follow-up experiments.

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