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
Descripción
Sumario: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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