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Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals

BACKGROUND: The usefulness of log(2 )transformation for cDNA microarray data has led to its widespread application to Affymetrix data. For Affymetrix data, where absolute intensities are indicative of number of transcripts, there is a systematic relationship between variance and magnitude of measure...

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Autores principales: Archer, Kellie J, Dumur, Catherine I, Ramakrishnan, Viswanathan
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2004
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC419979/
https://www.ncbi.nlm.nih.gov/pubmed/15147579
http://dx.doi.org/10.1186/1471-2105-5-60
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author Archer, Kellie J
Dumur, Catherine I
Ramakrishnan, Viswanathan
author_facet Archer, Kellie J
Dumur, Catherine I
Ramakrishnan, Viswanathan
author_sort Archer, Kellie J
collection PubMed
description BACKGROUND: The usefulness of log(2 )transformation for cDNA microarray data has led to its widespread application to Affymetrix data. For Affymetrix data, where absolute intensities are indicative of number of transcripts, there is a systematic relationship between variance and magnitude of measurements. Application of the log(2 )transformation expands the scale of genes with low intensities while compressing the scale of genes with higher intensities thus reversing the mean by variance relationship. The usefulness of these transformations needs to be examined. RESULTS: Using an Affymetrix GeneChip(® )dataset, problems associated with applying the log(2 )transformation to absolute intensity data are demonstrated. Use of the spread-versus-level plot to identify an appropriate variance stabilizing transformation is presented. For the data presented, the spread-versus-level plot identified a power transformation that successfully stabilized the variance of probe set summaries. CONCLUSION: The spread-versus-level plot is helpful to identify transformations for variance stabilization. This is robust against outliers and avoids assumption of models and maximizations.
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spelling pubmed-4199792004-06-04 Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals Archer, Kellie J Dumur, Catherine I Ramakrishnan, Viswanathan BMC Bioinformatics Methodology Article BACKGROUND: The usefulness of log(2 )transformation for cDNA microarray data has led to its widespread application to Affymetrix data. For Affymetrix data, where absolute intensities are indicative of number of transcripts, there is a systematic relationship between variance and magnitude of measurements. Application of the log(2 )transformation expands the scale of genes with low intensities while compressing the scale of genes with higher intensities thus reversing the mean by variance relationship. The usefulness of these transformations needs to be examined. RESULTS: Using an Affymetrix GeneChip(® )dataset, problems associated with applying the log(2 )transformation to absolute intensity data are demonstrated. Use of the spread-versus-level plot to identify an appropriate variance stabilizing transformation is presented. For the data presented, the spread-versus-level plot identified a power transformation that successfully stabilized the variance of probe set summaries. CONCLUSION: The spread-versus-level plot is helpful to identify transformations for variance stabilization. This is robust against outliers and avoids assumption of models and maximizations. BioMed Central 2004-05-17 /pmc/articles/PMC419979/ /pubmed/15147579 http://dx.doi.org/10.1186/1471-2105-5-60 Text en Copyright © 2004 Archer et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
spellingShingle Methodology Article
Archer, Kellie J
Dumur, Catherine I
Ramakrishnan, Viswanathan
Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals
title Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals
title_full Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals
title_fullStr Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals
title_full_unstemmed Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals
title_short Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals
title_sort graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC419979/
https://www.ncbi.nlm.nih.gov/pubmed/15147579
http://dx.doi.org/10.1186/1471-2105-5-60
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