Software and tools for microarray data analysis

Jai Prakash Mehta, Sweta Rani

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

12 Citations (Scopus)


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.

Original languageEnglish
Title of host publicationGene Expression Profiling
Subtitle of host publicationMethods and Protocols
EditorsLorraine O'Driscoll
Number of pages13
Publication statusPublished - 2011
Externally publishedYes

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Classification
  • Clustering
  • Gene expression
  • Gene ontology
  • Microarray
  • Normalization
  • Pathways


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