Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data

Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data

SUMMARY We introduce a novel Matlab toolbox for microarray data analysis. This toolbox uses normalization based upon a normally distributed background and differential gene expression based on five statistical measures. The objects in this toolbox are open source and can be implemented to suit your application. AVAILABILITY MDAT v1.0 is a Matlab toolbox and requires Matlab to run. MDAT is fre...

cDNA Microarray Data Normalization

Normalization methods for analysis of microarray gene-expression data.

This paper investigates subset normalization to adjust for location biases (e.g., splotches) combined with global normalization for intensity biases (e.g., saturation). A data set from a toxicogenomic experiment using the same control and the same treated sample hybridized to six different microarrays is used to contrast the different normalization methods. Simple t-tests were used to compare t...

Normalization and Differential Gene Expression Analysis of Microarray Data

DNA microarray technologies have the capability of simultaneously measuring the abundance of thousands of mRNA-sequences. Analysis of microarray data involves many different steps such as image analysis, background correction, and normaliza-tion, but also more classical statistical analysis such as testing for significant differences between groups of arrays. The work presented in this thesis i...

Data Analysis: Microarray Gene Expression

Most genomic data within the NextBio platform are generated using the Affymetrix platform (Figure 2). Ideally, all Affymetrix data would be imported as CEL files, and processed using the same normalization method, such as Robust Multi-array Average (RMA)1; however, for pre-existing experiments, this is often impossible. In this case, probeset-level Microarray Suite version 5 (MAS5) intensities2...