Microarray analysis, pre-processing. Quality in the selection of differentiatedly expressed genes
Following the success of microarray technology, in the literature there is a large number of experiments made with them. However, the problems of standardization and the many sources of variability make it necessary posteriori validation techniques. For this reason, we have tried to study how the se...
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| Formato: | Artículo revista |
| Lenguaje: | Español |
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Escuela de Perfeccionamiento en Investigación Operativa
2018
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| Acceso en línea: | https://revistas.unc.edu.ar/index.php/epio/article/view/20345 |
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I10-R359-article-20345 |
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Universidad Nacional de Córdoba |
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I-10 |
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R-359 |
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Revista de la Escuela de Perfeccionamiento en Investigación Operativa |
| language |
Español |
| format |
Artículo revista |
| topic |
microarrays optimización de procesos mejora de la calidad microarrays process optimization quality improvement |
| spellingShingle |
microarrays optimización de procesos mejora de la calidad microarrays process optimization quality improvement Ruiz Ruiz, Nuria Redchuk, Andrés Moguerza, Javier M. Microarray analysis, pre-processing. Quality in the selection of differentiatedly expressed genes |
| topic_facet |
microarrays optimización de procesos mejora de la calidad microarrays process optimization quality improvement |
| author |
Ruiz Ruiz, Nuria Redchuk, Andrés Moguerza, Javier M. |
| author_facet |
Ruiz Ruiz, Nuria Redchuk, Andrés Moguerza, Javier M. |
| author_sort |
Ruiz Ruiz, Nuria |
| title |
Microarray analysis, pre-processing. Quality in the selection of differentiatedly expressed genes |
| title_short |
Microarray analysis, pre-processing. Quality in the selection of differentiatedly expressed genes |
| title_full |
Microarray analysis, pre-processing. Quality in the selection of differentiatedly expressed genes |
| title_fullStr |
Microarray analysis, pre-processing. Quality in the selection of differentiatedly expressed genes |
| title_full_unstemmed |
Microarray analysis, pre-processing. Quality in the selection of differentiatedly expressed genes |
| title_sort |
microarray analysis, pre-processing. quality in the selection of differentiatedly expressed genes |
| description |
Following the success of microarray technology, in the literature there is a large number of experiments made with them. However, the problems of standardization and the many sources of variability make it necessary posteriori validation techniques. For this reason, we have tried to study how the selection of genes influence some key preprocessing techniques. Many of the studies conducted to compare these techniques have been carried out on experiments which optimal results are known a priori to try to determine which has greater accuracy. In our case, we do not know the correct result a priori and what has been accomplished is a comparative analysis of the results obtained in each case in order to predict a priori the behavior of each of the techniques discussed in terms of various factors as initial data distribution, expression patterns object of interest, the presence of outliers, and so on.Three techniques have been applied on the preprocessing on a microarray experiment. The techniques are GCRMA, MAS5 and MBEI. In our data there have been found mainly three patterns of expression in those genes expressed and have been shown statistically that there is an association between the pre-processing technique used and the predominant pattern in it. This trend is related to efficiency in the detection of outliers and the magnitude of change detected with each of them. So far, it has not been able to establish a statistically significant in confirming the agreement between the three methods after the selection of differentially expressed genes. |
| publisher |
Escuela de Perfeccionamiento en Investigación Operativa |
| publishDate |
2018 |
| url |
https://revistas.unc.edu.ar/index.php/epio/article/view/20345 |
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AT ruizruiznuria microarrayanalysispreprocessingqualityintheselectionofdifferentiatedlyexpressedgenes AT redchukandres microarrayanalysispreprocessingqualityintheselectionofdifferentiatedlyexpressedgenes AT moguerzajavierm microarrayanalysispreprocessingqualityintheselectionofdifferentiatedlyexpressedgenes AT ruizruiznuria analisisdemicroarrayspreprocesocalidadenlaselecciondegenesdiferencialmenteexpresados AT redchukandres analisisdemicroarrayspreprocesocalidadenlaselecciondegenesdiferencialmenteexpresados AT moguerzajavierm analisisdemicroarrayspreprocesocalidadenlaselecciondegenesdiferencialmenteexpresados |
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2024-09-03T22:23:17Z |
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2024-09-03T22:23:17Z |
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1809215334585991168 |
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I10-R359-article-203452018-06-18T15:15:55Z Microarray analysis, pre-processing. Quality in the selection of differentiatedly expressed genes Análisis de microarrays, preproceso. Calidad en la selección de genes diferencialmente expresados Ruiz Ruiz, Nuria Redchuk, Andrés Moguerza, Javier M. microarrays optimización de procesos mejora de la calidad microarrays process optimization quality improvement Following the success of microarray technology, in the literature there is a large number of experiments made with them. However, the problems of standardization and the many sources of variability make it necessary posteriori validation techniques. For this reason, we have tried to study how the selection of genes influence some key preprocessing techniques. Many of the studies conducted to compare these techniques have been carried out on experiments which optimal results are known a priori to try to determine which has greater accuracy. In our case, we do not know the correct result a priori and what has been accomplished is a comparative analysis of the results obtained in each case in order to predict a priori the behavior of each of the techniques discussed in terms of various factors as initial data distribution, expression patterns object of interest, the presence of outliers, and so on.Three techniques have been applied on the preprocessing on a microarray experiment. The techniques are GCRMA, MAS5 and MBEI. In our data there have been found mainly three patterns of expression in those genes expressed and have been shown statistically that there is an association between the pre-processing technique used and the predominant pattern in it. This trend is related to efficiency in the detection of outliers and the magnitude of change detected with each of them. So far, it has not been able to establish a statistically significant in confirming the agreement between the three methods after the selection of differentially expressed genes. Como consecuencia del éxito de la tecnología de microarrays, aparecen en la literatura un gran número de experimentos realizados con los mismos. Sin embargo los problemas de estandarización y las numerosas fuentes de variabilidad hacen necesarias técnicas de validación a posteriori. Por este motivo se ha tratado de estudiar cómo influye en la selección de genes diferencialmente expresados algunas de las principales técnicas de preproceso. Muchos de los estudios realizados para comparar estas técnicas, se han llevado a cabo sobre experimentos cuyos resultados óptimos se conocen a priori con el fin de intentar determinar cuál presenta mayor precisión. En nuestro caso no conocemos el resultado correcto a priori y lo que se ha realizado es un análisis comparativo de los resultados obtenidos en cada caso con el fin de poder predecir el comportamiento a priori de cada una de las técnicas analizadas en función de diversos factores como distribución de los datos iniciales, patrones de expresión objeto de interés, presencia de outliers, etc.Se han aplicado tres técnicas de preproceso sobre un experimento de microarrays. Las técnicas aplicadas son GCRMA, MBEI y MAS5. Se han encontrado en nuestros datos principalmente tres patrones de expresión en aquellos genes diferencialmente expresados y se ha demostrado estadísticamente que existe una asociación entre la técnica de preproceso utilizada y el patrón predominante en la misma. Esta tendencia se ha relacionado con la eficiencia en la detección de valores atípicos y con la magnitud de cambio detectada con cada una de ellas. Por el momento, no se ha podido establecer un estadístico significativo a la hora de confirmar la concordancia entre los tres métodos tras la selección de genes diferencialmente expresados. Escuela de Perfeccionamiento en Investigación Operativa 2018-06-18 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion application/pdf https://revistas.unc.edu.ar/index.php/epio/article/view/20345 Revista de la Escuela de Perfeccionamiento en Investigación Operativa; Vol. 20 Núm. 33 (2012): Octubre; 72-88 1853-9777 0329-7322 spa https://revistas.unc.edu.ar/index.php/epio/article/view/20345/19976 |