Computational protocol: Discovering biological connections between experimental conditions based on common patterns of differential gene expression

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Protocol publication

[…] All computations were performed in the R programming environment (version 2.11.1). The R packages affy [] and limma [] were obtained from Bioconductor (http://www.bioconductor.org) and the package multtest [] was obtained from the Comprehensive R Archive Network (CRAN) (http://cran.r-project.org). Entrez Gene ID-specific probeset mappings for Affymetrix arrays (version 13.0.0) [] were obtained from the Molecular and Behavioral Neuroscience Institute at the University of Michigan (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF). All computations were performed using the Linux cluster for Genetic Analysis (LinGA) at the Boston University Medical Campus. […]

Pipeline specifications

Software tools affy, limma, multtest
Databases Gene
Application Gene expression microarray analysis
Organisms Homo sapiens
Diseases Breast Neoplasms, Melanoma
Chemicals Estradiol, Estrogens