Results 1 - 10 of 780

Exploration, normalization, and summaries of high density oligonucleotide array probe level data.

by Rafael A Irizarry , Bridget Hobbs , Francois Collin , Yasmin D Beazer-Barclay , Kristen J Antonellis , Uwe Scherf , Terence P Speed - Biostatistics, , 2003
"... SUMMARY In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip R system with the objective of improving upon currently used measures of gene expression. Our analyses make use of three data sets: a small experimental study consisting of f ..."
Abstract - Cited by 854 (33 self) - Add to MetaCart
SUMMARY In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip R system with the objective of improving upon currently used measures of gene expression. Our analyses make use of three data sets: a small experimental study consisting

Model-Based Analysis of Oligonucleotide Arrays: Model Validation, Design Issues and Standard Error Application

by Cheng Li, Wing Hung Wong , 2001
"... Background: A model-based analysis of oligonucleotide expression arrays we developed previously uses a probe-sensitivity index to capture the response characteristic of a specific probe pair and calculates model-based expression indexes (MBEI). MBEI has standard error attached to it as a measure of ..."
Abstract - Cited by 775 (28 self) - Add to MetaCart
Background: A model-based analysis of oligonucleotide expression arrays we developed previously uses a probe-sensitivity index to capture the response characteristic of a specific probe pair and calculates model-based expression indexes (MBEI). MBEI has standard error attached to it as a measure

oligonucleotide arrays: a multiplicative noise

by E. Calvo, J. Corbeil
"... Statistical analysis of high-density ..."
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Statistical analysis of high-density

Empirical Bayes Analysis of a Microarray Experiment

by Bradley Efron, Robert Tibshirani, John D. Storey, Virginia Tusher - Journal of the American Statistical Association , 2001
"... Microarrays are a novel technology that facilitates the simultaneous measurement of thousands of gene expression levels. A typical microarray experiment can produce millions of data points, raising serious problems of data reduction, and simultaneous inference. We consider one such experiment in whi ..."
Abstract - Cited by 492 (20 self) - Add to MetaCart
in which oligonucleotide arrays were employed to assess the genetic effects of ionizing radiation on seven thousand human genes. A simple nonparametric empirical Bayes model is introduced, which is used to guide the ef � cient reduction of the data to a single summary statistic per gene, and also to make

Summaries of Affymetrix GeneChip probe level data

by Rafael A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs, Terence P. Speed - Nucleic Acids Res , 2003
"... High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11±20 pairs of pr ..."
Abstract - Cited by 471 (21 self) - Add to MetaCart
High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11±20 pairs

From features to expression: High-density oligonucleotide array analysis revisited.

by Félix Naef, Daniel A. Lim, Nila Patil, Marcelo O. Magnasco , 2001
"... One of the most popular tools for large scale gene expression studies are high-density oligonucleotide #GeneChip r # # arrays. These currently have 16-20 small probe cells ##features## for evaluating the transcript abundance of each gene. In addition, each probe is accompanied by a mismatched ..."
Abstract - Cited by 13 (3 self) - Add to MetaCart
One of the most popular tools for large scale gene expression studies are high-density oligonucleotide #GeneChip r # # arrays. These currently have 16-20 small probe cells ##features## for evaluating the transcript abundance of each gene. In addition, each probe is accompanied by a mismatched

Joint Estimation of Calibration and Expression for High-Density Oligonucleotide Arrays

by Ann L. Oberg, Douglas W. Mahoney, Karla V. Ballman, Terry M. Therneau , 2006
"... Motivation: The need for normalization in microarray experiments has been well documented in the literature. Currently, most analysis methods treat normalization and analysis as a series of steps, with summarized data carried forward to the next step. Results: We present a unified algorithm which in ..."
Abstract - Cited by 1 (1 self) - Add to MetaCart
incorporates normalization and class comparison in one analysis using probe level perfect match and mismatch data. The algorithm is based on calibration models common to most biological assays, and the resulting chip-specific parameters have a natural interpretation. We show that the algorithm fits

A comparison of statistical methods for analysis of high density oligonucleotide array data

by Dilip Rajagopalan - Bioinformatics , 2003
"... Motivation: Gene expression profiling has become an invaluable tool in functional genomics. A wide variety of statistical methods have been employed to analyze the data generated in experiments using Affymetrix GeneChip R © microarrays. It is important to understand the relative performance of these ..."
Abstract - Cited by 34 (0 self) - Add to MetaCart
Motivation: Gene expression profiling has become an invaluable tool in functional genomics. A wide variety of statistical methods have been employed to analyze the data generated in experiments using Affymetrix GeneChip R © microarrays. It is important to understand the relative performance

Statistical analysis of high density oligonucleotide arrays: a SAFER approach

by Daniel Holder, Richard F. Raubertas, V. Bill Pikounis, Vladimir Svetnik, Keith Soper , 2001
"... probe-specific effects High-density oligonucleotide arrays allow researchers to measure mRNA transcript abundance for thousands of genes on a single array. The large number of genes, multiple sources of variation, and typically small number of experimental units (EUs) combine to make analysis of dat ..."
Abstract - Cited by 25 (0 self) - Add to MetaCart
probe-specific effects High-density oligonucleotide arrays allow researchers to measure mRNA transcript abundance for thousands of genes on a single array. The large number of genes, multiple sources of variation, and typically small number of experimental units (EUs) combine to make analysis

Flexible use of high-density oligonucleotide arrays for singlenucleotide polymorphism discovery and validation,”

by Shoulian Dong , Eugene Wang , Linda Hsie , Yanxiang Cao , Xiaogiong Chen , Thomas R Gingeras - Genome Research, , 2001
"... A method for identifying and validating single nucleotide polymorphisms (SNPs) with high-density oligonucleotide arrays without the need for locus-specific polymerase chain reactions (PCR) is described in this report. Genomic DNAs were divided into subsets with complexity of ∼10 Mb by restriction e ..."
Abstract - Cited by 16 (2 self) - Add to MetaCart
A method for identifying and validating single nucleotide polymorphisms (SNPs) with high-density oligonucleotide arrays without the need for locus-specific polymerase chain reactions (PCR) is described in this report. Genomic DNAs were divided into subsets with complexity of ∼10 Mb by restriction
Results 1 - 10 of 780