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Software and Tools for Microarray Data Analysis

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 784)

Abstract

A typical microarray experiment results in series of images, depending on the experimental design and number of samples. Software analyses the images to obtain the intensity at each spot and quantify the expression for each transcript. This is followed by normalization, and then various data analysis techniques are applied on the data. The whole analysis pipeline requires a large number of software to accurately handle the massive amount of data. Fortunately, there are large number of freely available and commercial software to churn the massive amount of data to manageable sets of differentially expressed genes, functions, and pathways. This chapter describes the software and tools which can be used to analyze the gene expression data right from the image analysis to gene list, ontology, and pathways.

Key words

Microarray Gene expression Normalization Clustering Classification Gene ontology Pathways 
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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Conway InstituteUniversity College DublinDublinIreland
  2. 2.School of Pharmacy & Pharmaceutical SciencesPanoz Institute, Trinity College DublinDublinIreland

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