Assessing numerical dependence in gene expression summaries with the jackknife expression difference.

Statistical methods to test for differential expression traditionally assume that each gene's expression summaries are independent across arrays. When certain preprocessing methods are used to obtain those summaries, this assumption is not necessarily true. In general, the erroneous assumption...

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Autores principales:	John R Stevens, Gabriel Nicholas
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1538c3076a5d4a84a04095707f5293e1
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id	oai:doaj.org-article:1538c3076a5d4a84a04095707f5293e1
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spelling	oai:doaj.org-article:1538c3076a5d4a84a04095707f5293e12021-11-18T07:09:59ZAssessing numerical dependence in gene expression summaries with the jackknife expression difference.1932-620310.1371/journal.pone.0039570https://doaj.org/article/1538c3076a5d4a84a04095707f5293e12012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22876276/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Statistical methods to test for differential expression traditionally assume that each gene's expression summaries are independent across arrays. When certain preprocessing methods are used to obtain those summaries, this assumption is not necessarily true. In general, the erroneous assumption of dependence results in a loss of statistical power. We introduce a diagnostic measure of numerical dependence for gene expression summaries from any preprocessing method and discuss the relative performance of several common preprocessing methods with respect to this measure. Some common preprocessing methods introduce non-trivial levels of numerical dependence. The issue of (between-array) dependence has received little if any attention in the literature, and researchers working with gene expression data should not take such properties for granted, or they risk unnecessarily losing statistical power.John R StevensGabriel NicholasPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e39570 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q John R Stevens Gabriel Nicholas Assessing numerical dependence in gene expression summaries with the jackknife expression difference.
description	Statistical methods to test for differential expression traditionally assume that each gene's expression summaries are independent across arrays. When certain preprocessing methods are used to obtain those summaries, this assumption is not necessarily true. In general, the erroneous assumption of dependence results in a loss of statistical power. We introduce a diagnostic measure of numerical dependence for gene expression summaries from any preprocessing method and discuss the relative performance of several common preprocessing methods with respect to this measure. Some common preprocessing methods introduce non-trivial levels of numerical dependence. The issue of (between-array) dependence has received little if any attention in the literature, and researchers working with gene expression data should not take such properties for granted, or they risk unnecessarily losing statistical power.
format	article
author	John R Stevens Gabriel Nicholas
author_facet	John R Stevens Gabriel Nicholas
author_sort	John R Stevens
title	Assessing numerical dependence in gene expression summaries with the jackknife expression difference.
title_short	Assessing numerical dependence in gene expression summaries with the jackknife expression difference.
title_full	Assessing numerical dependence in gene expression summaries with the jackknife expression difference.
title_fullStr	Assessing numerical dependence in gene expression summaries with the jackknife expression difference.
title_full_unstemmed	Assessing numerical dependence in gene expression summaries with the jackknife expression difference.
title_sort	assessing numerical dependence in gene expression summaries with the jackknife expression difference.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/1538c3076a5d4a84a04095707f5293e1
work_keys_str_mv	AT johnrstevens assessingnumericaldependenceingeneexpressionsummarieswiththejackknifeexpressiondifference AT gabrielnicholas assessingnumericaldependenceingeneexpressionsummarieswiththejackknifeexpressiondifference
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Assessing numerical dependence in gene expression summaries with the jackknife expression difference.

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