Spot defects detection in cDNA microarray images
- Autores
- Larese, Monica Graciela; Granitto, Pablo Miguel; Gomez, Juan Carlos
- Año de publicación
- 2011
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Bad quality spots should be filtered out at early steps in microarray analysis to avoid noisy data. In this paper we implement quality control of individual spots from real microarray images. First of all, we consider the binary classification problem of detecting bad quality spots. We propose the use of ensemble algorithms to perform detection and obtain improved accuracies over previous studies in the literature. Next, we analyze the untackled problem of identifying specific spot defects. One spot may have several faults simultaneously (or none of them) yielding a multi-label classification problem. We propose several extra features in addition to those used for binary classification, and we use three different methods to perform the classification task: five independent binary classifiers, the recent Convex Multi-task Feature Learning (CMFL) algorithm and Convex Multi-task Independent Learning (CMIL). We analyze the Hamming loss and areas under the receiver operating characteristic (ROC) curves to quantify the accuracies of the methods. We find that the three strategies achieve similar results leading to a successful identification of particular defects. Also, using a Random forest-based analysis we show that the newly introduced features are highly relevant for this task.
Fil: Larese, Monica Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; Argentina
Fil: Granitto, Pablo Miguel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; Argentina
Fil: Gomez, Juan Carlos. Universidad Nacional de Rosario. Facultad de Ciencias Exactas, Ingeniería y Agrimensura. Escuela de Ingeniería Electrónica. Departamento de Control. Laboratorio de Sistemas Dinámicos y Procesamiento de Información; Argentina - Materia
-
MICROARRAY IMAGES
QUALITY CONTROL
DEFECTS IDENTIFICATION
ENSEMBLE CLASSIFIERS
CONVEX MULTI-TASK LEARNING
PATTERN RECOGNITION - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/113381
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Spot defects detection in cDNA microarray imagesLarese, Monica GracielaGranitto, Pablo MiguelGomez, Juan CarlosMICROARRAY IMAGESQUALITY CONTROLDEFECTS IDENTIFICATIONENSEMBLE CLASSIFIERSCONVEX MULTI-TASK LEARNINGPATTERN RECOGNITIONhttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1https://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1Bad quality spots should be filtered out at early steps in microarray analysis to avoid noisy data. In this paper we implement quality control of individual spots from real microarray images. First of all, we consider the binary classification problem of detecting bad quality spots. We propose the use of ensemble algorithms to perform detection and obtain improved accuracies over previous studies in the literature. Next, we analyze the untackled problem of identifying specific spot defects. One spot may have several faults simultaneously (or none of them) yielding a multi-label classification problem. We propose several extra features in addition to those used for binary classification, and we use three different methods to perform the classification task: five independent binary classifiers, the recent Convex Multi-task Feature Learning (CMFL) algorithm and Convex Multi-task Independent Learning (CMIL). We analyze the Hamming loss and areas under the receiver operating characteristic (ROC) curves to quantify the accuracies of the methods. We find that the three strategies achieve similar results leading to a successful identification of particular defects. Also, using a Random forest-based analysis we show that the newly introduced features are highly relevant for this task.Fil: Larese, Monica Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; ArgentinaFil: Granitto, Pablo Miguel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; ArgentinaFil: Gomez, Juan Carlos. Universidad Nacional de Rosario. Facultad de Ciencias Exactas, Ingeniería y Agrimensura. Escuela de Ingeniería Electrónica. Departamento de Control. Laboratorio de Sistemas Dinámicos y Procesamiento de Información; ArgentinaSpringer2011-08info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/113381Larese, Monica Graciela; Granitto, Pablo Miguel; Gomez, Juan Carlos; Spot defects detection in cDNA microarray images; Springer; Pattern Analysis And Applications; 16; 3; 8-2011; 307-3191433-7541CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1007/s10044-011-0234-xinfo:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007/s10044-011-0234-xinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:56:33Zoai:ri.conicet.gov.ar:11336/113381instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:56:34.142CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Spot defects detection in cDNA microarray images |
title |
Spot defects detection in cDNA microarray images |
spellingShingle |
Spot defects detection in cDNA microarray images Larese, Monica Graciela MICROARRAY IMAGES QUALITY CONTROL DEFECTS IDENTIFICATION ENSEMBLE CLASSIFIERS CONVEX MULTI-TASK LEARNING PATTERN RECOGNITION |
title_short |
Spot defects detection in cDNA microarray images |
title_full |
Spot defects detection in cDNA microarray images |
title_fullStr |
Spot defects detection in cDNA microarray images |
title_full_unstemmed |
Spot defects detection in cDNA microarray images |
title_sort |
Spot defects detection in cDNA microarray images |
dc.creator.none.fl_str_mv |
Larese, Monica Graciela Granitto, Pablo Miguel Gomez, Juan Carlos |
author |
Larese, Monica Graciela |
author_facet |
Larese, Monica Graciela Granitto, Pablo Miguel Gomez, Juan Carlos |
author_role |
author |
author2 |
Granitto, Pablo Miguel Gomez, Juan Carlos |
author2_role |
author author |
dc.subject.none.fl_str_mv |
MICROARRAY IMAGES QUALITY CONTROL DEFECTS IDENTIFICATION ENSEMBLE CLASSIFIERS CONVEX MULTI-TASK LEARNING PATTERN RECOGNITION |
topic |
MICROARRAY IMAGES QUALITY CONTROL DEFECTS IDENTIFICATION ENSEMBLE CLASSIFIERS CONVEX MULTI-TASK LEARNING PATTERN RECOGNITION |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.2 https://purl.org/becyt/ford/1 https://purl.org/becyt/ford/1.2 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
Bad quality spots should be filtered out at early steps in microarray analysis to avoid noisy data. In this paper we implement quality control of individual spots from real microarray images. First of all, we consider the binary classification problem of detecting bad quality spots. We propose the use of ensemble algorithms to perform detection and obtain improved accuracies over previous studies in the literature. Next, we analyze the untackled problem of identifying specific spot defects. One spot may have several faults simultaneously (or none of them) yielding a multi-label classification problem. We propose several extra features in addition to those used for binary classification, and we use three different methods to perform the classification task: five independent binary classifiers, the recent Convex Multi-task Feature Learning (CMFL) algorithm and Convex Multi-task Independent Learning (CMIL). We analyze the Hamming loss and areas under the receiver operating characteristic (ROC) curves to quantify the accuracies of the methods. We find that the three strategies achieve similar results leading to a successful identification of particular defects. Also, using a Random forest-based analysis we show that the newly introduced features are highly relevant for this task. Fil: Larese, Monica Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; Argentina Fil: Granitto, Pablo Miguel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; Argentina Fil: Gomez, Juan Carlos. Universidad Nacional de Rosario. Facultad de Ciencias Exactas, Ingeniería y Agrimensura. Escuela de Ingeniería Electrónica. Departamento de Control. Laboratorio de Sistemas Dinámicos y Procesamiento de Información; Argentina |
description |
Bad quality spots should be filtered out at early steps in microarray analysis to avoid noisy data. In this paper we implement quality control of individual spots from real microarray images. First of all, we consider the binary classification problem of detecting bad quality spots. We propose the use of ensemble algorithms to perform detection and obtain improved accuracies over previous studies in the literature. Next, we analyze the untackled problem of identifying specific spot defects. One spot may have several faults simultaneously (or none of them) yielding a multi-label classification problem. We propose several extra features in addition to those used for binary classification, and we use three different methods to perform the classification task: five independent binary classifiers, the recent Convex Multi-task Feature Learning (CMFL) algorithm and Convex Multi-task Independent Learning (CMIL). We analyze the Hamming loss and areas under the receiver operating characteristic (ROC) curves to quantify the accuracies of the methods. We find that the three strategies achieve similar results leading to a successful identification of particular defects. Also, using a Random forest-based analysis we show that the newly introduced features are highly relevant for this task. |
publishDate |
2011 |
dc.date.none.fl_str_mv |
2011-08 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/113381 Larese, Monica Graciela; Granitto, Pablo Miguel; Gomez, Juan Carlos; Spot defects detection in cDNA microarray images; Springer; Pattern Analysis And Applications; 16; 3; 8-2011; 307-319 1433-7541 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/113381 |
identifier_str_mv |
Larese, Monica Graciela; Granitto, Pablo Miguel; Gomez, Juan Carlos; Spot defects detection in cDNA microarray images; Springer; Pattern Analysis And Applications; 16; 3; 8-2011; 307-319 1433-7541 CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/doi/10.1007/s10044-011-0234-x info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007/s10044-011-0234-x |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
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openAccess |
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https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
Springer |
publisher.none.fl_str_mv |
Springer |
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reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
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CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
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