lumi is a

free Free may refer to: Concept * Freedom, having the ability to do something, without having to obey anyone/anything * Freethought, a position that beliefs should be formed only on the basis of logic, reason, and empiricism * Emancipate, to procur ...

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and open development software project for the analysis and comprehension of Illumina expression and methylation microarray data. The project was started in the summer of 2006 and set out to provide algorithms and data management tools of Illumina in the framework of

Bioconductor Bioconductor is a Free software, free, Open-source software, open source and Open source software development, open development software project for the analysis and comprehension of Genome, genomic data generated by Wet laboratory, wet lab experi ...

. It is based on the

statistical Statistics (from German: ''Statistik'', "description of a state, a country") is the discipline that concerns the collection, organization, analysis, interpretation, and presentation of data. In applying statistics to a scientific, industria ...

R programming language R is a programming language for statistical computing and graphics supported by the R Core Team and the R Foundation for Statistical Computing. Created by statisticians Ross Ihaka and Robert Gentleman, R is used among data miners, bioinform ...

Features

The lumi package provides an analysis pipeline for probe-level Illumina expression and methylation microarray data, including probe-identifier management ( nuID), updated probe-to-gene mapping and annotation using the latest release of RefSeq (nuIDblast), probe-intensity transformation (VST) and normalization (RSN), quality control (QA/QC) and preprocessing methods specific for Illumina methylation data. By extending the ExprSet object with Illumina-specific features, lumi is designed to work with other Bioconductor packages, such as Limma and GOstats to detect differential genes and conduct Gene Ontology analysis.

History

The lumi project was started in the summer of 2006 at the Bioinformatics Core Facility of the

Robert H. Lurie Comprehensive Cancer Center The Robert H. Lurie Comprehensive Cancer Center of Northwestern University (Lurie Cancer Center), is a National Cancer Institute (NCI)-designated Comprehensive Cancer Center located on Northwestern Memorial Hospital's downtown medical campus in ...

Northwestern University Northwestern University is a private research university in Evanston, Illinois. Founded in 1851, Northwestern is the oldest chartered university in Illinois and is ranked among the most prestigious academic institutions in the world. Charte ...

. Originally lumi was designed for the analysis of Illumina Expression BeadArray data. Starting from 2010 (version > 2.0), functions of analyzing Illumina methylation microarray data was added. The project team consists of Drs. Pan Du, Simon M. Lin, and Warren A. Kibbe. The project was started upon a request for collaboration from Dr. Serdar E. Bulun to analyze a set of new Illumina microarray data acquired at his lab on the study of the effect of retinoic acids on cancers. Dr. Pan Du led the software development of the project. lumi was the first software package to utilize the unique design of redundancy of beadArrays for the data transformation and normalization processes. The first release of lumi was on January 3, 2007 through the

website. Before its formal release, it was beta-tested at Norwegian Radiumhospital, Leiden University Medical Center, Universiteit van Amsterdam, Università degli Studi di Brescia, UC Davis, Wayne State University, NIH, M.D. Anderson Cancer Center, Case Western Reserve University, Harvard University, Washington University, and Walter and Eliza Hall Institute of Medical Research.

External links

lumi software release website

Old lumi Website

Official Bioconductor Website
{{R (programming language) Free science software Free R (programming language) software Microarrays

Features

History

See also

External links