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The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data

BACKGROUND: High-throughput systems are powerful tools for the life science research community. The complexity and volume of data from these systems, however, demand special treatment. Graphical tools are needed to evaluate many aspects of the data throughout the analysis process because plots can p...

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Detalles Bibliográficos
Autores principales: Woody, Owen Z, Nadon, Robert
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1679802/
https://www.ncbi.nlm.nih.gov/pubmed/17147786
http://dx.doi.org/10.1186/1751-0473-1-6
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author Woody, Owen Z
Nadon, Robert
author_facet Woody, Owen Z
Nadon, Robert
author_sort Woody, Owen Z
collection PubMed
description BACKGROUND: High-throughput systems are powerful tools for the life science research community. The complexity and volume of data from these systems, however, demand special treatment. Graphical tools are needed to evaluate many aspects of the data throughout the analysis process because plots can provide quality assessments for thousands of values simultaneously. The utility of a plot, in turn, is contingent on both its interpretability and its efficiency. RESULTS: The shivplot, a graphical technique motivated by microarrays but applicable to any replicated high-throughput data set, is described. The plot capitalizes on the strengths of three well-established plotting graphics – a boxplot, a distribution density plot, and a variability vs intensity plot – by effectively combining them into a single representation. CONCLUSION: The utility of the new display is illustrated with microarray data sets. The proposed graph, retaining all the information of its precursors, conserves space and minimizes redundancy, but also highlights features of the data that would be difficult to appreciate from the individual display components. We recommend the use of the shivplot both for exploratory data analysis and for the communication of experimental data in publications.
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spelling pubmed-16798022006-12-02 The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data Woody, Owen Z Nadon, Robert Source Code Biol Med Methodology BACKGROUND: High-throughput systems are powerful tools for the life science research community. The complexity and volume of data from these systems, however, demand special treatment. Graphical tools are needed to evaluate many aspects of the data throughout the analysis process because plots can provide quality assessments for thousands of values simultaneously. The utility of a plot, in turn, is contingent on both its interpretability and its efficiency. RESULTS: The shivplot, a graphical technique motivated by microarrays but applicable to any replicated high-throughput data set, is described. The plot capitalizes on the strengths of three well-established plotting graphics – a boxplot, a distribution density plot, and a variability vs intensity plot – by effectively combining them into a single representation. CONCLUSION: The utility of the new display is illustrated with microarray data sets. The proposed graph, retaining all the information of its precursors, conserves space and minimizes redundancy, but also highlights features of the data that would be difficult to appreciate from the individual display components. We recommend the use of the shivplot both for exploratory data analysis and for the communication of experimental data in publications. BioMed Central 2006-11-08 /pmc/articles/PMC1679802/ /pubmed/17147786 http://dx.doi.org/10.1186/1751-0473-1-6 Text en Copyright © 2006 Woody and Nadon; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology
Woody, Owen Z
Nadon, Robert
The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data
title The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data
title_full The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data
title_fullStr The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data
title_full_unstemmed The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data
title_short The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data
title_sort shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data
topic Methodology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1679802/
https://www.ncbi.nlm.nih.gov/pubmed/17147786
http://dx.doi.org/10.1186/1751-0473-1-6
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