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

Selection and validation of normalization methods for c-DNA microarrays using within-array replications. Research Abstract Details 

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Selection and validation of normalization methods for c-DNA microarrays using within-array replications. Abstract Text:

Jianqing Fan,Yue Niu,

MOTIVATION: Normalization of microarray data is essential for multiple-array analyses. Several normalization protocols have been proposed based on different biological or statistical assumptions. A fundamental problem arises whether they have effectively normalized arrays. In addition, for a given array, the question arises how to choose a method to most effectively normalize the microarray data. 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 chi approximation. With estimated P-values, we can choose a most appropriate method to normalize a specific 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 a large number of clones with replications, a customized microarray experiment carrying just a few hundred genes on the study of the molecular roles of Interferons on tumor, and the Agilent microarrays carrying tens of thousands of total RNA samples in the MAQC project on the study of reproducibility, sensitivity and specificity of the data. AVAILABILITY: Code to implement the method in the statistical package R is available from the authors.

Selection and validation of normalization methods for c-DNA microarrays using within-array replications. Publishing Authors By Initials

J Fan,Y Niu,

For similar geographic locations: americas: north america: united states research abstracts see: geographic locations: americas: north america: united states research

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Selection and validation of normalization methods for c-DNA microarrays using within-array replications. Journal Published:

PUBLICATION TYPE: Validation Studies

Journal: Bioinformatics (Oxford, England)

VOLUME: 23

Page Numbers: 2391-8

Journal Abbreviation: Bioinformatics

ISSN: 1460-2059

DAY: 27

MONTH: 07

YEAR: 2007

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

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LANGUAGE: eng

NlmUniqueID: 9808944

Selection and validation of normalization methods for c-DNA microarrays using within-array replications. Keywords Mesh Terms:

KEYWORDS: United States

MESH TERMS: methods

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Grant and Affiliation Information for Selection and validation of normalization methods for c-DNA microarrays using within-array replications.

AFFILIATION: Department of Operations Research and Financial Engineering Princeton University, Princeton, NJ 08544, USA. jqfan@princeton.edu

Country: England

AGENCY: United States NIGMS

GRANT: R01-GM072611

ACRONYM: GM

MEDLINETA: Bioinformatics

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