A Two-Way Semi-Linear Model for Normalization and Significant Analysis of cDNA Microarray Data
نویسنده
چکیده
A basic question in analyzing cDNA microarray data is normalization. The purpose of normalization is to remove systematic bias in the observed expression values by establishing a normalization curve across the whole dynamic range. A proper normalization procedure ensures that the normalized intensity ratios provide meaningful measures of relative expression levels. We propose a two-way semi-linear model (TW-SLM) for normalization and significant analysis of microarray data. This method does not make the usual assumptions underlying some of the existing methods. For example, it does not assume that: (i) the percentage of differentially expressed genes is small; or (ii) there is symmetry in the expression levels of upand down-regulated genes, as required in the lowess normalization method. The TW-SLM also naturally incorporates uncertainty due to normalization into significant analysis of microarrays. We use a semiparametric approach based on polynomial splines in the TW-SLM to estimate the normalization curves and the normalized expression values. We also conduct simulation studies to evaluate the TW-SLM method and illustrate the proposed method using a published microarray data set.
منابع مشابه
A Semi-linear Model for Normalization and Analysis of cDNA Microarray Data
Motivation: Microarray analysis is a technology for monitoring gene expression levels on a large scale and has been widely used in functional genomics. A challenging issue in the analysis of microarray data is normalization. A proper normalization procedure ensures that the intensity ratios provide meaningful measures of relative expression levels. There are two important questions concerning n...
متن کاملPackage ‘ twslm ’ April 19 , 2009
April 19, 2009 Version 1.0.2 Date 2007-07-13 Maintainer Deli Wang Author Deli Wang, Jian Huang Depends splines Title A two-way semilinear model for normalization and analysis of cDNA microarray data. Description twslm is for normalization of cDNA microarray data with the two-way semilinear model. Huber’s and Tukey’s bisquare weight functions are available for robust esti...
متن کاملPackage ‘ TwslmSpikeWeight ’ April 17 , 2009
April 17, 2009 Version 1.0.1 Date 2006-01-17 Maintainer Deli Wang Author Deli Wang, Jian Huang Depends splines Title Systematic approaches using TW-SLM for incorporating control spots and data quality information to improve normalization of cDNA microarray data. Description TwslmSpikeWeight is for normalization of cDNA microarray data with the two-way semilinear model(TW...
متن کاملNormalization Benefits Microarray-Based Classification
When using cDNA microarrays, normalization to correct labeling bias is a common preliminary step before further data analysis is applied, its objective being to reduce the variation between arrays. To date, assessment of the effectiveness of normalization has mainly been confined to the ability to detect differentially expressed genes. Since a major use of microarrays is the expression-based ph...
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تاریخ انتشار 2005