Normalisation of Multicondition cDNA Macroarray Data

Background. Normalisation is a critical step in obtaining meaningful information from the high-dimensional DNA array data. This is particularly important when complex biological hypotheses/questions, such a functional analysis and regulatory interactions within biological systems, are investigated....

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Main Authors:	Dawes, Nicola L., Glassey, Jarka
Format:	Online
Language:	English
Published:	Hindawi Publishing Corporation 2007
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1872052/

id	pubmed-1872052
recordtype	oai_dc
spelling	pubmed-18720522007-05-30 Normalisation of Multicondition cDNA Macroarray Data Dawes, Nicola L. Glassey, Jarka Research Article Background. Normalisation is a critical step in obtaining meaningful information from the high-dimensional DNA array data. This is particularly important when complex biological hypotheses/questions, such a functional analysis and regulatory interactions within biological systems, are investigated. A nonparametric, intensity-dependent normalisation method based on global identification of self-consistent set (SCS) of genes is proposed here for such systems. Results. The SCS normalisation is introduced and its behaviour demonstrated for a range of user-defined parameters affecting its performance. It is compared to a standard global normalisation method in terms of noise reduction and signal retention. Conclusions. The SCS normalisation results using 16 macroarray data sets from a Bacillus subtilis experiment confirm that the method is capable of reducing undesirable experimental variation whilst retaining important biological information. The ease and speed of implementation mean that this method can be easily adapted to other multicondition time/strain series single colour array data. Hindawi Publishing Corporation 2007 2007-04-22 /pmc/articles/PMC1872052/ /pubmed/17538691 http://dx.doi.org/10.1155/2007/90578 Text en Copyright © 2007 N. L. Dawes and J. Glassey. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Dawes, Nicola L. Glassey, Jarka
spellingShingle	Dawes, Nicola L. Glassey, Jarka Normalisation of Multicondition cDNA Macroarray Data
author_facet	Dawes, Nicola L. Glassey, Jarka
author_sort	Dawes, Nicola L.
title	Normalisation of Multicondition cDNA Macroarray Data
title_short	Normalisation of Multicondition cDNA Macroarray Data
title_full	Normalisation of Multicondition cDNA Macroarray Data
title_fullStr	Normalisation of Multicondition cDNA Macroarray Data
title_full_unstemmed	Normalisation of Multicondition cDNA Macroarray Data
title_sort	normalisation of multicondition cdna macroarray data
description	Background. Normalisation is a critical step in obtaining meaningful information from the high-dimensional DNA array data. This is particularly important when complex biological hypotheses/questions, such a functional analysis and regulatory interactions within biological systems, are investigated. A nonparametric, intensity-dependent normalisation method based on global identification of self-consistent set (SCS) of genes is proposed here for such systems. Results. The SCS normalisation is introduced and its behaviour demonstrated for a range of user-defined parameters affecting its performance. It is compared to a standard global normalisation method in terms of noise reduction and signal retention. Conclusions. The SCS normalisation results using 16 macroarray data sets from a Bacillus subtilis experiment confirm that the method is capable of reducing undesirable experimental variation whilst retaining important biological information. The ease and speed of implementation mean that this method can be easily adapted to other multicondition time/strain series single colour array data.
publisher	Hindawi Publishing Corporation
publishDate	2007
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1872052/
_version_	1611396584720826368

Normalisation of Multicondition cDNA Macroarray Data

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