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mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data
Mass spectrometry (MS) data are used to analyze biological phenomena based on chemical species. However, these data often contain unexpected duplicate records and missing values due to technical or biological factors. These ‘dirty data’ problems increase the difficulty of performing MS analyses beca...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5494294/ https://www.ncbi.nlm.nih.gov/pubmed/28680817 http://dx.doi.org/10.1002/2211-5463.12247 |
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author | Lee, Geunho Lee, Hyun Beom Jung, Byung Hwa Nam, Hojung |
author_facet | Lee, Geunho Lee, Hyun Beom Jung, Byung Hwa Nam, Hojung |
author_sort | Lee, Geunho |
collection | PubMed |
description | Mass spectrometry (MS) data are used to analyze biological phenomena based on chemical species. However, these data often contain unexpected duplicate records and missing values due to technical or biological factors. These ‘dirty data’ problems increase the difficulty of performing MS analyses because they lead to performance degradation when statistical or machine‐learning tests are applied to the data. Thus, we have developed missing values preprocessor (mvp), an open‐source software for preprocessing data that might include duplicate records and missing values. mvp uses the property of MS data in which identical chemical species present the same or similar values for key identifiers, such as the mass‐to‐charge ratio and intensity signal, and forms cliques via graph theory to process dirty data. We evaluated the validity of the mvp process via quantitative and qualitative analyses and compared the results from a statistical test that analyzed the original and mvp‐applied data. This analysis showed that using mvp reduces problems associated with duplicate records and missing values. We also examined the effects of using unprocessed data in statistical tests and examined the improved statistical test results obtained with data preprocessed using mvp. |
format | Online Article Text |
id | pubmed-5494294 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-54942942017-07-05 mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data Lee, Geunho Lee, Hyun Beom Jung, Byung Hwa Nam, Hojung FEBS Open Bio Method Mass spectrometry (MS) data are used to analyze biological phenomena based on chemical species. However, these data often contain unexpected duplicate records and missing values due to technical or biological factors. These ‘dirty data’ problems increase the difficulty of performing MS analyses because they lead to performance degradation when statistical or machine‐learning tests are applied to the data. Thus, we have developed missing values preprocessor (mvp), an open‐source software for preprocessing data that might include duplicate records and missing values. mvp uses the property of MS data in which identical chemical species present the same or similar values for key identifiers, such as the mass‐to‐charge ratio and intensity signal, and forms cliques via graph theory to process dirty data. We evaluated the validity of the mvp process via quantitative and qualitative analyses and compared the results from a statistical test that analyzed the original and mvp‐applied data. This analysis showed that using mvp reduces problems associated with duplicate records and missing values. We also examined the effects of using unprocessed data in statistical tests and examined the improved statistical test results obtained with data preprocessed using mvp. John Wiley and Sons Inc. 2017-06-19 /pmc/articles/PMC5494294/ /pubmed/28680817 http://dx.doi.org/10.1002/2211-5463.12247 Text en © 2017 The Authors. Published by FEBS Press and John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Method Lee, Geunho Lee, Hyun Beom Jung, Byung Hwa Nam, Hojung mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data |
title |
mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data |
title_full |
mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data |
title_fullStr |
mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data |
title_full_unstemmed |
mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data |
title_short |
mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data |
title_sort | mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5494294/ https://www.ncbi.nlm.nih.gov/pubmed/28680817 http://dx.doi.org/10.1002/2211-5463.12247 |
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