Intensity Dependent Confidence Intervals on Microarray Measurements of Differentially Expressed Genes: A Case Study of the Effect of MK5, FKRP and TAF4 on the Transcriptome

To perform a quantitative analysis with gene-arrays, one must take into account inaccuracies (experimental variations, biological variations and other measurement errors) which are seldom known. In this paper we investigated amplification and noise propagation related errors by measuring intensity d...

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Detalles Bibliográficos
Autores principales: Van Belle, Werner, Gerits, Nancy, Jakobsen, Kirsti, Brox, Vigdis, Van Ghelue, Marijke, Moens, Ugo
Formato: Texto
Lenguaje:English
Publicado: Libertas Academica 2007
Materias:
Original Research
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759122/
https://www.ncbi.nlm.nih.gov/pubmed/19936079
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author Van Belle, Werner
Gerits, Nancy
Jakobsen, Kirsti
Brox, Vigdis
Van Ghelue, Marijke
Moens, Ugo
author_facet Van Belle, Werner
Gerits, Nancy
Jakobsen, Kirsti
Brox, Vigdis
Van Ghelue, Marijke
Moens, Ugo
author_sort Van Belle, Werner
collection PubMed
description To perform a quantitative analysis with gene-arrays, one must take into account inaccuracies (experimental variations, biological variations and other measurement errors) which are seldom known. In this paper we investigated amplification and noise propagation related errors by measuring intensity dependent variations. Based on a set of control samples, we create confidence intervals for up and down regulations. We validated our method through a qPCR experiment and compared it to standard analysis methods (including loess normalization and filtering methods based on genetic variability). The results reveal that amplification related errors are a major concern.
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spelling pubmed-27591222009-11-23 Intensity Dependent Confidence Intervals on Microarray Measurements of Differentially Expressed Genes: A Case Study of the Effect of MK5, FKRP and TAF4 on the Transcriptome Van Belle, Werner Gerits, Nancy Jakobsen, Kirsti Brox, Vigdis Van Ghelue, Marijke Moens, Ugo Gene Regul Syst Bio Original Research To perform a quantitative analysis with gene-arrays, one must take into account inaccuracies (experimental variations, biological variations and other measurement errors) which are seldom known. In this paper we investigated amplification and noise propagation related errors by measuring intensity dependent variations. Based on a set of control samples, we create confidence intervals for up and down regulations. We validated our method through a qPCR experiment and compared it to standard analysis methods (including loess normalization and filtering methods based on genetic variability). The results reveal that amplification related errors are a major concern. Libertas Academica 2007-07-17 /pmc/articles/PMC2759122/ /pubmed/19936079 Text en © 2007 The authors. http://creativecommons.org/licenses/by/3.0 This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Original Research
Van Belle, Werner
Gerits, Nancy
Jakobsen, Kirsti
Brox, Vigdis
Van Ghelue, Marijke
Moens, Ugo
Intensity Dependent Confidence Intervals on Microarray Measurements of Differentially Expressed Genes: A Case Study of the Effect of MK5, FKRP and TAF4 on the Transcriptome
title Intensity Dependent Confidence Intervals on Microarray Measurements of Differentially Expressed Genes: A Case Study of the Effect of MK5, FKRP and TAF4 on the Transcriptome
title_full Intensity Dependent Confidence Intervals on Microarray Measurements of Differentially Expressed Genes: A Case Study of the Effect of MK5, FKRP and TAF4 on the Transcriptome
title_fullStr Intensity Dependent Confidence Intervals on Microarray Measurements of Differentially Expressed Genes: A Case Study of the Effect of MK5, FKRP and TAF4 on the Transcriptome
title_full_unstemmed Intensity Dependent Confidence Intervals on Microarray Measurements of Differentially Expressed Genes: A Case Study of the Effect of MK5, FKRP and TAF4 on the Transcriptome
title_short Intensity Dependent Confidence Intervals on Microarray Measurements of Differentially Expressed Genes: A Case Study of the Effect of MK5, FKRP and TAF4 on the Transcriptome
title_sort intensity dependent confidence intervals on microarray measurements of differentially expressed genes: a case study of the effect of mk5, fkrp and taf4 on the transcriptome
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759122/
https://www.ncbi.nlm.nih.gov/pubmed/19936079
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