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Use of within-array replicate spots for assessing differential expression in microarray experiments. (2005)

by Smyth GK, J Michaud, Scott HS
Venue:Bioinformatics
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Limma: linear models for microarray data

by Gordon K. Smyth, Matthew Ritchie, Natalie Thorne, James Wettenhall, Wei Shi - Bioinformatics and Computational Biology Solutions using R and Bioconductor , 2005
"... This free open-source software implements academic research by the authors and co-workers. If you use it, please support the project by citing the appropriate journal articles listed in Section 2.1.Contents ..."
Abstract - Cited by 774 (13 self) - Add to MetaCart
This free open-source software implements academic research by the authors and co-workers. If you use it, please support the project by citing the appropriate journal articles listed in Section 2.1.Contents
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...hematical assumptions which are never exactly true for microarray data. It has been argued that the p-values are useful for ranking genes even in the presence of large deviations from the assumptions =-=[6, 2]-=-. Benjamini and Hochberg’s control of the false discovery rate assumes independence between genes, although Reiner et al [7] have argued that it works for many forms of dependence as well. The B-stati...

limma powers differential expression analyses for RNA-sequencing and microarray studies

by Matthew E. Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W. Law, Wei Shi, Gordon K. Smyth - Nucleic Acids Res , 2015
"... RNA-sequencing and microarray studies (Article begins on next page) The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters. ..."
Abstract - Cited by 32 (4 self) - Add to MetaCart
RNA-sequencing and microarray studies (Article begins on next page) The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters.
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...ure is then incorporated into the linear model fit and hence into all tests for DE. Originally the idea was used to estimate the correlation between replicate copies of the same probe on a microarray =-=(44)-=-. The correlation strategy preserves more information than simply averaging the replicate probe copies. More generally, the same idea is also used to model the correlation between related RNA samples,...

Interferome v2.0: an updated database of annotated interferon-regulated genes. Nucleic Acids Res 41: D1040–1046

by Irina Rusinova, Sam Forster, Simon Yu, Anitha Kannan, Marion Masse, Helen Cumming, Ross Chapman, Paul J. Hertzog , 2013
"... Interferome v2.0 ..."
Abstract - Cited by 15 (1 self) - Add to MetaCart
Interferome v2.0
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...on to the 75th percentile was performed to remove technical variations between individual arrays. Data from two-colour arrays were normalized applying normalizeWithinArrays and normalizeBetweenArrays =-=(26,27)-=-. Data from any replicated probes were averaged to provide a single measure for each probe in the array. All Agilent control probes were removed. Normalized probes from both microarray platforms were ...

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia

by Yair Benita, Hirotoshi Kikuchi, Andrew D. Smith, Michael Q. Zhang, Daniel C. Chung, Ramnik J. Xavier - Nucleic Acids Res , 2009
"... that form the core response to hypoxia ..."
Abstract - Cited by 13 (0 self) - Add to MetaCart
that form the core response to hypoxia
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... mean for each probe with replicates. Only probes for which the expression values of the replicates were all positive or all negative were further tested for differential expression. The Limma module =-=(41)-=- of biocoductor was used to fit a linear model for each probe and P-values were corrected using the false discovery rate method (42). Promoters Promoter sequences of human genome build 18 were obtaine...

doi:10.1093/nar/gkl435 Non-linear analysis of GeneChip arrays

by Diana Abdueva, Dmitriy Skvortsov, Simon Tavaré , 2006
"... The application of microarray hybridization theory to Affymetrix GeneChip data has been a recent focus for data analysts. It has been shown that the hyperbolic Langmuir isotherm captures the shape of the signal response to concentration of Affymetrix GeneChips. We demonstrate that existing linear fi ..."
Abstract - Cited by 7 (0 self) - Add to MetaCart
The application of microarray hybridization theory to Affymetrix GeneChip data has been a recent focus for data analysts. It has been shown that the hyperbolic Langmuir isotherm captures the shape of the signal response to concentration of Affymetrix GeneChips. We demonstrate that existing linear fit methods for extracting gene expression measures are not well adapted for the effect of saturation resulting from surface adsorption processes. In contrast to the most popular methods, we fit background and concentration parameters within a single global fitting routine instead of estimating the background before obtaining gene expression measures. We describe a non-linear multi-chip model of the perfect match signal that effectively allows for the separation of specific and non-specific components of the microarray signal and avoids saturation bias in the high-intensity range. Multimodel inference, incorporated within the fitting routine, allows a quantitative selection of the model that best describes the observed data. The performance of this method is evaluated on publicly available datasets, and comparisons to popular algorithms are presented.
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...lts from the Affycomp assessment of HG-U133A and HG-U95 spike-in data, processed with NLFIT (submitted August 19, 2005) Statistics HG_U95 HG_U133A 1. [26] Median SD—median SD across replicates — — 2. =-=[18]-=- Null log-fc IQR—Inter-quartile range of the log-fold-changes from genes that should not change — — 3. [20] Null log-fc 99.9%—99.9% percentile of the log-fold-changes if from the genes that should not...

Function of the cytochrome bc1-aa3 branch of the respiratory network in mycobacteria and network adaptation occurring in response to its disruption

by Limenako G. Matsoso, Bavesh D. Kana, Paul K. Crellin, David J. Lea-smith, Assunta Pelosi, David Powell, Stephanie S. Dawes, Harvey Rubin, Valerie Mizrahi, Limenako G. Matsoso, Bavesh D. Kana, Paul K. Crellin, David J. Lea-smith, Assunta Pelosi, David Powell, Stephanie S. Dawes, Harvey Rubin, Valerie Mizrahi - J. Bacteriol. 2005
"... Supplemental material This article cites 39 articles, 15 of which can be accessed free at: ..."
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Supplemental material This article cites 39 articles, 15 of which can be accessed free at:
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...-absolutedeviation (MAD). The normalized data were then used to fit a linear model (43) for each gene using generalized least-squares, which takes into account the correlation between duplicate spots =-=(33)-=-. The coefficient of the fitted model for each gene describes the inferred difference in RNA expression between wild-type and mutant cells. Empirical Bayes was then used to calculate the moderated t D...

Selection and validation of normalization methods for c-DNA microarrays using within-array replications

by Jianqing Fan, Yue Niu , 2007
"... Motivation:Normalizationofmicroarraydataisessentialformultiplearray analyses. Several normalization protocols have been proposed basedondifferentbiologicalorstatisticalassumptions.Afundamental problem arises whether they have effectively normalized arrays. In addition, for agiven array, the question ..."
Abstract - Cited by 5 (0 self) - Add to MetaCart
Motivation:Normalizationofmicroarraydataisessentialformultiplearray analyses. Several normalization protocols have been proposed basedondifferentbiologicalorstatisticalassumptions.Afundamental problem arises whether they have effectively normalized arrays. In addition, for agiven array, the question arises how to choose a methodtomosteffectivelynormalizethemicroarraydata. Results: We propose several techniques to compare the effectiveness of different normalization methods. We approach the problem by constructing statistics to test whether there are any systematic biases in the expression profiles among duplicated spots within an array. The test statistics involve estimating the genewise variances. This is accomplished by using several novel methods, including empirical Bayes methods for moderating the genewise variances and the smoothing methods for aggregating variance information. P-values are estimated based on a normal or chisquare approximation. With estimated P-values, we can choose a most appropriate method to normalize aspecific array and assess the extent to which the systematic biases due to the variations of experimental conditions have been removed. The effectiveness and validity of the proposed methods are convincingly illustrated by a carefully designed simulation study. The method is further illustrated by an application to human placenta cDNAs comprising alarge number of clones with replications, acustomized microarray experiment carrying just afew hundred genes on the study of the molecular roles of Interferons on tumor, and the Agilent microarrays carryingtensofthousandsoftotalRNAsamplesintheMAQCproject on thestudyofreproducibility,sensitivityandspecificityofthe data.

Ecf, an Alternative Sigma Factor from Neisseria gonorrhoeae, Controls Expression of msrAB, Which Encodes Methionine Sulfoxide Reductase

by Ishara C. Gunesekere, Charlene M. Kahler, Catherine S. Ryan, Lori A. S. Snyder, Nigel J. Saunders, Julian I. Rood, John K. Davies , 2005
"... A DNA microarray was used to identify genes transcribed in Neisseria gonorrhoeae using Ecf, an alternative sigma factor. No differences between the transcriptional profiles of strain FA1090 and a mutant where ecf had been inactivated could be detected when both were grown in vitro. We therefore cons ..."
Abstract - Cited by 5 (1 self) - Add to MetaCart
A DNA microarray was used to identify genes transcribed in Neisseria gonorrhoeae using Ecf, an alternative sigma factor. No differences between the transcriptional profiles of strain FA1090 and a mutant where ecf had been inactivated could be detected when both were grown in vitro. We therefore constructed a gonococcal strain in which Ecf can be overexpressed. Some differentially expressed genes are clustered with ecf on the genome and appear to form a single transcriptional unit. Expression of the gene encoding MsrAB, which possesses methionine sulfoxide reductase activity, was also dependent on Ecf, suggesting that the regulon responds to oxidative damage. Western blotting confirmed that the increased level of MsrAB protein is dependent on the presence of Ecf. Bacterial sigma factors are essential components of the RNA polymerase holoenzyme and determine promoter selectivity and specificity. Bacteria usually contain at least one essential sigma factor, sigma-70, which is necessary for cell viability, as well as a number of accessory sigma factors that are often involved in responses to environmental stimuli or the phase of growth. The relative amount of RNA polymerase holoenzyme containing each sigma factor determines the amplitude
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...bsolute-deviation. The normalized data were then used to fit a linear model (23) for each gene using a generalized least-squares method which took into account the correlation between replicate spots =-=(24)-=-. The coefficient of the fitted model for each gene describes the inferred difference in RNA expression between the two strains. Empirical Bayes method was then used to calculate the moderated t stati...

BioMed Central

by Bmc Microbiology, Qingmin Wu, Jianwu Pei, Carol Turse, Thomas A Ficht, Thomas A Ficht , 2006
"... Research article Mariner mutagenesis of Brucella melitensis reveals genes with previously uncharacterized roles in virulence and survival ..."
Abstract - Cited by 4 (0 self) - Add to MetaCart
Research article Mariner mutagenesis of Brucella melitensis reveals genes with previously uncharacterized roles in virulence and survival
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...y real-time RT-PCR in biofilm compared with planktonic cultures. The data are expressed as the means and standard deviations of at least two biologically independent experiments. correlation function =-=[60]-=- available in LIMMA to acquire an approximation of gene-by-gene variance. This method greatly improves the precision with which the gene-wise variances are estimated and thereby maximizes inference me...

Global transcription and metabolic flux analysis of Escherichia coli in glucose-limited fedbatch cultivations. Appl Environ Microbiol 74: 7002–7015

by K. Lemuth, T. Hardiman, S. Winter, D. Pfeiffer, M. A. Keller, S. Lange, M. Reuss, R. D. Schmid, M. Siemann-herzberg, K. Lemuth, T. Hardiman, S. Winter, D. Pfeiffer, M. A. Keller, S. Lange, M. Reuss, R. D. Schmid, M. Siemann-herzberg , 2008
"... This article cites 69 articles, 23 of which can be accessed free ..."
Abstract - Cited by 4 (0 self) - Add to MetaCart
This article cites 69 articles, 23 of which can be accessed free
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