title: TM4 microarray software suite.
abstract: Powerful specialized software is essential for managing, quantifying, and ultimately deriving scientific insight from results of a microarray experiment. We have developed a suite of software applications, known as TM4, to support such gene expression studies. The suite consists of open-source tools for data management and reporting, image analysis, normalization and pipeline control, and data mining and visualization. An integrated MIAME-compliant MySQL database is included. This chapter describes each component of the suite and includes a sample analysis walk-through.
authors.affiliation: Department of Bioinformatics, The Institute for Genomic Research, Rockville, MD, USA.
authors.forename: Alexander I
authors.initials: AI
authors.lastname: Saeed
authors.forename: Nirmal K
authors.initials: NK
authors.lastname: Bhagabati
authors.forename: John C
authors.initials: JC
authors.lastname: Braisted
authors.forename: Wei
authors.initials: W
authors.lastname: Liang
authors.forename: Vasily
authors.initials: V
authors.lastname: Sharov
authors.forename: Eleanor A
authors.initials: EA
authors.lastname: Howe
authors.forename: Jianwei
authors.initials: J
authors.lastname: Li
authors.forename: Mathangi
authors.initials: M
authors.lastname: Thiagarajan
authors.forename: Joseph A
authors.initials: JA
authors.lastname: White
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
mesh_terms: D000465:Algorithms; D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods / Q000706:statistics & numerical data; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data; D012984:Software