Cargando…
NITPicker: selecting time points for follow-up experiments
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 desig...
Autores principales: | , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444531/ https://www.ncbi.nlm.nih.gov/pubmed/30940082 http://dx.doi.org/10.1186/s12859-019-2717-5 |
_version_ | 1783408044584992768 |
---|---|
author | Ezer, Daphne Keir, Joseph |
author_facet | Ezer, Daphne Keir, Joseph |
author_sort | Ezer, Daphne |
collection | PubMed |
description | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-019-2717-5) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6444531 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-64445312019-04-11 NITPicker: selecting time points for follow-up experiments Ezer, Daphne Keir, Joseph BMC Bioinformatics Methodology Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-019-2717-5) contains supplementary material, which is available to authorized users. BioMed Central 2019-04-02 /pmc/articles/PMC6444531/ /pubmed/30940082 http://dx.doi.org/10.1186/s12859-019-2717-5 Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Methodology Article Ezer, Daphne Keir, Joseph NITPicker: selecting time points for follow-up experiments |
title | NITPicker: selecting time points for follow-up experiments |
title_full | NITPicker: selecting time points for follow-up experiments |
title_fullStr | NITPicker: selecting time points for follow-up experiments |
title_full_unstemmed | NITPicker: selecting time points for follow-up experiments |
title_short | NITPicker: selecting time points for follow-up experiments |
title_sort | nitpicker: selecting time points for follow-up experiments |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444531/ https://www.ncbi.nlm.nih.gov/pubmed/30940082 http://dx.doi.org/10.1186/s12859-019-2717-5 |
work_keys_str_mv | AT ezerdaphne nitpickerselectingtimepointsforfollowupexperiments AT keirjoseph nitpickerselectingtimepointsforfollowupexperiments |