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Automating dChip: toward reproducible sharing of microarray data analysis

BACKGROUND: During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis software package accessible to both biologist and data analysts. However, cha...

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Detalles Bibliográficos
Autor principal: Li, Cheng
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390544/
https://www.ncbi.nlm.nih.gov/pubmed/18466620
http://dx.doi.org/10.1186/1471-2105-9-231
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author Li, Cheng
author_facet Li, Cheng
author_sort Li, Cheng
collection PubMed
description BACKGROUND: During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis software package accessible to both biologist and data analysts. However, challenges arise when dChip users want to analyze large number of arrays automatically and share data analysis procedures and parameters. Improvement is also needed when the dChip user support team tries to identify the causes of reported analysis errors or bugs from users. RESULTS: We report here implementation and application of the dChip automation module. Through this module, dChip automation files can be created to include menu steps, parameters, and data viewpoints to run automatically. A data-packaging function allows convenient transfer from one user to another of the dChip software, microarray data, and analysis procedures, so that the second user can reproduce the entire analysis session of the first user. An analysis report file can also be generated during an automated run, including analysis logs, user comments, and viewpoint screenshots. CONCLUSION: The dChip automation module is a step toward reproducible research, and it can prompt a more convenient and reproducible mechanism for sharing microarray software, data, and analysis procedures and results. Automation data packages can also be used as publication supplements. Similar automation mechanisms could be valuable to the research community if implemented in other genomics and bioinformatics software packages.
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spelling pubmed-23905442008-05-21 Automating dChip: toward reproducible sharing of microarray data analysis Li, Cheng BMC Bioinformatics Software BACKGROUND: During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis software package accessible to both biologist and data analysts. However, challenges arise when dChip users want to analyze large number of arrays automatically and share data analysis procedures and parameters. Improvement is also needed when the dChip user support team tries to identify the causes of reported analysis errors or bugs from users. RESULTS: We report here implementation and application of the dChip automation module. Through this module, dChip automation files can be created to include menu steps, parameters, and data viewpoints to run automatically. A data-packaging function allows convenient transfer from one user to another of the dChip software, microarray data, and analysis procedures, so that the second user can reproduce the entire analysis session of the first user. An analysis report file can also be generated during an automated run, including analysis logs, user comments, and viewpoint screenshots. CONCLUSION: The dChip automation module is a step toward reproducible research, and it can prompt a more convenient and reproducible mechanism for sharing microarray software, data, and analysis procedures and results. Automation data packages can also be used as publication supplements. Similar automation mechanisms could be valuable to the research community if implemented in other genomics and bioinformatics software packages. BioMed Central 2008-05-08 /pmc/articles/PMC2390544/ /pubmed/18466620 http://dx.doi.org/10.1186/1471-2105-9-231 Text en Copyright © 2008 Li; 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 Software
Li, Cheng
Automating dChip: toward reproducible sharing of microarray data analysis
title Automating dChip: toward reproducible sharing of microarray data analysis
title_full Automating dChip: toward reproducible sharing of microarray data analysis
title_fullStr Automating dChip: toward reproducible sharing of microarray data analysis
title_full_unstemmed Automating dChip: toward reproducible sharing of microarray data analysis
title_short Automating dChip: toward reproducible sharing of microarray data analysis
title_sort automating dchip: toward reproducible sharing of microarray data analysis
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390544/
https://www.ncbi.nlm.nih.gov/pubmed/18466620
http://dx.doi.org/10.1186/1471-2105-9-231
work_keys_str_mv AT licheng automatingdchiptowardreproduciblesharingofmicroarraydataanalysis