title: Analyzing and visualizing expression data with Spotfire.
abstract: This unit assumes the reader is familiar with the Spotfire environment, has successfully installed Spotfire, and has uploaded and prepared data for analysis. It presents numerous methods for analyzing microarray data. Specifically, the first two protocols describe methods for identifying differentially expressed genes via the t-test/ANOVA and the distinction calculation respectively. Another protocol discusses how to conduct a profile search. Additional protocols illustrate various clustering methods, such as hierarchical clustering, K-means clustering, and principal components analysis. A protocol explaining coincidence testing allows the reader to compare the results from multiple clustering methods. Additional protocols demonstrate querying the Internet for information based on the microarray data, mathematically transforming data within Spotfire to generate new data columns, and exporting Spotfire visualizations.
authors.affiliation: St Jude Children's Research Hospital, Memphis, Tennessee, USA.
authors.forename: Deepak
authors.initials: D
authors.lastname: Kaushal
authors.forename: Clayton W
authors.initials: CW
authors.lastname: Naeve
mesh_terms: D003196:Computer Graphics; D003628:Database Management Systems; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011381:Programming Languages; D012984:Software; D014584:User-Computer Interface