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NITPicker : selecting time points for follow-up experiments
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Ezer, Daphne and Keir, Joseph (2019) NITPicker : selecting time points for follow-up experiments. BMC Bioinformatics, 20 (1). 166. doi:10.1186/s12859-019-2717-5 ISSN 1471-2105.
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WRAP-NITPicker-selecting-time-points-experiments-Ezer-2019.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (1985Kb) | Preview |
Official URL: http://dx.doi.org/10.1186/s12859-019-2717-5
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.
| Item Type: | Journal Article | |||||||||||||||
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| Subjects: | H Social Sciences > HA Statistics Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software |
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Statistics | |||||||||||||||
| Library of Congress Subject Headings (LCSH): | Experimental design -- Software, Statistical decision -- Software | |||||||||||||||
| Journal or Publication Title: | BMC Bioinformatics | |||||||||||||||
| Publisher: | BioMed Central Ltd. | |||||||||||||||
| ISSN: | 1471-2105 | |||||||||||||||
| Official Date: | 2 April 2019 | |||||||||||||||
| Dates: |
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| Volume: | 20 | |||||||||||||||
| Number: | 1 | |||||||||||||||
| Article Number: | 166 | |||||||||||||||
| DOI: | 10.1186/s12859-019-2717-5 | |||||||||||||||
| Status: | Peer Reviewed | |||||||||||||||
| Publication Status: | Published | |||||||||||||||
| Access rights to Published version: | Open Access (Creative Commons) | |||||||||||||||
| Copyright Holders: | © The Author(s) 2019 | |||||||||||||||
| Date of first compliant deposit: | 11 April 2019 | |||||||||||||||
| Date of first compliant Open Access: | 11 April 2019 | |||||||||||||||
| RIOXX Funder/Project Grant: |
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